Date / Databases	Files / Description
2011/11/27: geneticcode	Minor change to add in release command for geneticcode
2011/11/27: 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
2010/10/11: system uniprot ipi	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
2010/10/07: taxonomy	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
2010/09/28: kegg	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
2010/09/21: kegg	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
2010/09/21: kegg	icarus/db/pathway.is
2010/09/21: hssp	Increased the number of parts used for indexing hssp
2010/09/21: hssp	icarus/db/hssp.i
2010/09/10: kegg	Support added to KEGGGENOME for KEYWORDS field
2010/09/10: kegg	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
2010/08/13: system	icarus/db/dbxref.i icarus/db/href.i
2010/08/13: dbest	Change to be more tolerant for non-standard characters in est names
2010/08/13: dbest	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
2010/08/12: genecards system	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
2010/08/05: 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
2010/06/18: system	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
2010/06/01: uniref	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
2010/05/21: system interpro iprmatches	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
2010/05/13: genecards system	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
2010/05/07: kegg	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
2010/05/04: system	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
2010/03/29: system	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
2010/03/05: system uniprot ipi	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)
2010/03/03: genpept	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
2010/02/11: system kegg	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
2010/01/26: system uniprot ipi	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
2010/01/26: genecards	icarus/db/genecards.it
2010/01/25: kegg	Removed a feature which is specific for srs8.2/srs8.3
2010/01/25: kegg	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
2010/01/21: unigene	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
2010/01/15: kegg	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.
2010/01/15: medline	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
2010/01/11: 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
2010/01/06: system kegg	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.
2009/12/18: genecards	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
2009/12/14: kegg	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
2009/12/09: kegg	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
2009/12/09: kegg	icarus/db/kegg_species.i
2009/12/08: pfam	Change needed to build read-links for pfamc
2009/12/08: pfam	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
2009/12/03: pfam	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
2009/12/03: medline	icarus/db/medlinecommon.i
2009/12/01: emboss	Minor change to allow colour postscript output for EMBOSS tools that produce colour graphics
2009/12/01: emboss	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
2009/11/23: kegg	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
2009/11/19: kegg	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
2009/10/30: kegg	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
2009/10/30: kegg	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
2009/10/22: entrezgene system	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
2009/10/21: kegg	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
2009/10/19: pfam	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
2009/10/15: system	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
2009/10/02: entrezgene	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
2009/09/17: refseq	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
2009/09/15: refseq	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
2009/09/14: interpro	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
2009/09/08: kegg	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
2009/09/04: system	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
2009/08/28: system kegg	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
2009/08/25: hmmer	icarus/db/hmmsearch.is
2009/08/25: uniprot ipi	Fix for a problem with indexing the ID field for uniprot
2009/08/25: uniprot ipi	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
2009/08/24: kegg	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
2009/08/04: system	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
2009/07/29: unigene uniprot	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
2009/07/23: homologene system	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
2009/07/23: unigene	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
2009/07/21: system uniprot ipi	icarus/db/dbxref.i icarus/db/swissprot.is
2009/07/21: cath	update for the new download site for cath data
2009/07/21: cath	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
2009/06/23: unigene	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
2009/06/19: system kegg	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 ":"
2009/06/11: hmmer	icarus/db/hmmsearch.is
2009/06/09: hmmer	Change to keep hmmsearch hit names short
2009/06/09: hmmer	icarus/db/hmmsearch.is
2009/06/02: medline	Change to handle a new layout used for some EC numbers in medline
2009/06/02: 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
2009/06/01: system	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
2009/05/08: system	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
2009/04/30: pdb	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
2009/04/16: system	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
2009/04/06: prosite	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
2009/03/23: genecards system	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
2009/03/16: 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
2009/03/12: genbank refseq	icarus/db/genbank.is icarus/db/genbankcommon.i
2009/03/11: prints	A small parser change for release 39 of PRINTS
2009/03/11: 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
2009/03/11: clustalw	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)
2009/03/10: fasta	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
2009/03/09: system	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.
2009/03/09: genbank refseq	icarus/db/genbank.is icarus/db/genbankcommon.i
2009/03/02: genbank refseq	Fix for a display issue with complete refseqp entries
2009/03/02: genbank refseq	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
2009/02/23: genbank	icarus/db/genbankwgs.it
2009/02/23: dbsts	Workaround for a few parsing errors during indexing
2009/02/23: dbsts	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
2009/02/13: system	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
2009/02/11: system	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
2009/01/27: system uniprot ipi	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
2009/01/20: pfam	icarus/db/swisspfam.it
2008/12/17: system	Added support for PRIDE and GeneCards hypertext links in uniprot
2008/12/17: system	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
2008/12/16: genbank refseq	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.
2008/12/09: embl	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
2008/12/03: embl genbank refseq	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.
2008/11/25: dbest	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.
2008/11/10: kegg system	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
2008/11/10: kegg	icarus/db/kegggenome.it
2008/11/10: dbest dbgss	Fix for a problem where SRS might mistake gzipped datafiles for actual datafiles
2008/11/10: dbest dbgss	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
2008/11/10: kegg	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
2008/11/10: entrezgene	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
2008/11/06: system	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
2008/11/06: genecards system	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
2008/10/16: uniprot ipi	icarus/db/swissprot.is
2008/10/10: go_xml	Small change to work around a dodgy data problem in the 20081005 release of go
2008/10/10: go_xml	icarus/db/go.is
2008/10/08: fasta	Change to handle a small data output change between fasta3.5.3 and fasta3.5.4
2008/10/08: fasta	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
2008/10/06: embl	icarus/db/emblnew.it icarus/db/emblnewfiles.it
2008/10/01: embl	removed a blast conversion section which had crept in
2008/10/01: embl	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
2008/09/24: system kegg	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
2008/09/19: system	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
2008/09/19: kegg	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
2008/09/15: embl	icarus/db/embl.is
2008/09/11: embl	Corrections for the annotated contig location and filenames used for deleted entries
2008/09/11: embl	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
2008/09/10: kegg	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
2008/08/22: emboss	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
2008/08/18: 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
2008/08/07: system uniprot ipi	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
2008/08/04: enzyme	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
2008/07/29: ensembl_mysql	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
2008/07/29: uniprot ipi	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
2008/07/29: system	icarus/db/dbxref.i icarus/db/href.i
2008/07/28: iprmatches	fix for links to prodom entries in iprmatches
2008/07/28: iprmatches	icarus/db/iprmatches.is
2008/07/02: kegg	Added support for the new Source and Component fields in the kegg drugs database (ldrug)
2008/07/02: kegg	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
2008/07/02: chebi	icarus/db/chebi_schema.i
2008/06/24: genecards	Change to allow for teh mew MilliPore references in GeneCards
2008/06/24: 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
2008/06/12: system	icarus/db/dbxref.i icarus/db/href.i
2008/06/09: kegg	fix for a problem with hypertext links from lenzyme to lcompound
2008/06/09: kegg	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
2008/06/02: embl genbank	icarus/db/emblrelease.i icarus/db/genbankrelease.i
2008/06/02: kegg	Fixed a parsing issue with the description line in some entries
2008/06/02: kegg	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
2008/05/27: system	icarus/db/dbxref.i
2008/05/14: system	Correction for coding error which would break sequence feature retrieval
2008/05/14: system	icarus/db/ftseq.is
2008/05/13: fasta	Change needed to handle some cases of output from fasta3.5
2008/05/13: fasta	icarus/db/fasta.is
2008/05/13: blast	Change to make sure blast honours a user request to use ungapped aligments
2008/05/13: blast	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
2008/05/12: kegg system	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
2008/05/12: kegg	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
2008/05/07: genbank embl refseq system	icarus/db/gbemblcommon.is icarus/db/href.i
2008/05/06: system	Added support for the new nmpdr link in uniprot
2008/05/06: system	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
2008/04/29: system	icarus/db/ftseq.is
2008/04/17: genecards system	Updates for version 2.38 of genecards
2008/04/17: genecards system	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
2008/04/01: fasta	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
2008/03/26: system	icarus/db/dbxref.i icarus/db/href.i
2008/03/20: ensembl_mysql	Changes for ensembl release 49
2008/03/20: ensembl_mysql	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
2008/03/18: chebi	icarus/db/chebidatamodel.i
2008/03/14: chebi	Changes for release 42 of chebi. A mass and charge field have been added
2008/03/14: chebi	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
2008/03/13: genecards	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
2008/03/05: genbank refseq medline	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
2008/02/29: system	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
2008/02/21: emboss	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)
2008/02/14: medline	icarus/db/medlinecommon.i
2008/02/07: system	Added support for the new world-2dpage link in uniprot
2008/02/07: system	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
2008/02/01: uniprot ipi	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
2008/01/25: system	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".
2008/01/18: emboss	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
2008/01/18: kegg	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
2008/01/17: system genbank embl refseq	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
2008/01/17: kegg	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
2008/01/03: geneseq	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.
2008/01/02: pdbfinder	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
2007/12/14: ensembl_mysql	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
2007/12/11: kegg	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
2007/11/29: kegg	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
2007/11/14: kegg	icarus/db/kegg_species.i icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/lcommon.is icarus/db/lenzyme.is
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
2007/11/08: genecards system	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
2007/11/06: cath	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
2007/11/06: entrezgene	icarus/db/entrezgene.is
2007/11/05: reactome	Added missing field definition
2007/11/05: reactome	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
2007/11/05: cath	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
2007/11/01: reactome	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
2007/10/31: system uniprot	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
2007/10/30: ensembl_mysql	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
2007/10/09: uniprot ipi	icarus/db/swissprot.is
2007/10/08: system uniprot ipi	Updated hypertext links for HGNC database
2007/10/08: system uniprot ipi	icarus/db/href.i icarus/db/swissprot.is
2007/09/27: chebi	Schema update for Chebi release 37. There are no major changes
2007/09/27: chebi	icarus/db/chebi_schema.i
2007/09/25: genbank refseq	Correction for an error in the creation date production
2007/09/25: genbank refseq	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
2007/09/24: system	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
2007/09/17: genbank refseq	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
2007/09/14: genbank refseq	icarus/db/genbankcommon.i
2007/09/10: pdbfinder	Added explanation of the ATOM and SEQRES fields
2007/09/10: pdbfinder	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
2007/09/07: embl genbank refseq system	icarus/db/emblcommon.i icarus/db/emblnew.i icarus/db/emblnewfiles.it icarus/db/emblrelease.i icarus/db/gbemblcommon.is icarus/db/general.it
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
2007/09/05: genbank embl refseq	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
2007/09/05: refseq	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
2007/09/03: genbank refseq	icarus/db/genbank.is
2007/08/30: transfac	Minor fix for sequence comment html link
2007/08/30: transfac	icarus/db/tffactor.is
2007/08/23: geneseq	Added a space between consecutive GO identifiers to improve web display
2007/08/23: geneseq	icarus/db/geneseq.is
2007/08/23: geneseq	Added support for additional external DB links
2007/08/23: geneseq	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
2007/08/21: genbank embl refseq system	icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/general.it icarus/db/srsgen.i
2007/08/21: clustalw	Changed srs 8.2 value to valStr for Iterative option
2007/08/21: clustalw	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
2007/08/21: entrezgene	icarus/db/entrezgene.is
2007/08/21: clustalw	Fix to remove multiple line breaks that shouldn't be present
2007/08/21: clustalw	icarus/db/clustalw.i icarus/db/nclustalw.i
2007/08/20: unigene	Removed links definition for SwissProt databases, added definition for UNIPROT virtual database
2007/08/20: unigene	icarus/db/unigene.i
2007/08/20: go_xml	Updated GO ftp location to point ftp.geneontology.org
2007/08/20: go_xml	icarus/db/go.it
2007/08/16: ensembl_mysql	Some minor changes for ensembl version 46
2007/08/16: ensembl_mysql	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
2007/08/15: embl	icarus/db/emblnew.it icarus/db/emblnewfiles.it
2007/08/14: pdb	Added support for the MODRES fields in the Entry view
2007/08/14: pdb	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
2007/08/14: pdb	icarus/db/pdb.is
2007/08/13: ensembl_mysql	Correct formatting for non-named protein domain list feature table
2007/08/13: ensembl_mysql	srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
2007/08/10: pdb	Added support for multiple entries in SPRSDE line
2007/08/10: pdb	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
2007/08/09: clustalw	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
2007/08/03: genbank refseq	icarus/db/genbank.is
2007/08/03: pdb	Correction for the searchname used by prisma for pdbmodel on the download site
2007/08/03: pdb	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
2007/08/01: embl genbank genecards interpro medline refseq	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
2007/08/01: kegg	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
2007/08/01: domo	icarus/db/domo.it
2007/08/01: embl	Change to include the expanded and annotated contig files in the embl updates.
2007/08/01: embl	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
2007/08/01: system	icarus/db/dbxref.i
2007/08/01: embl	Fix for a problem with constructing contig sequences when tincaching is enabled
2007/08/01: embl	icarus/db/embl.is
2007/08/01: kegg	updated kegg species mapping file
2007/08/01: kegg	icarus/db/kegg_species.i
2007/07/31: geneseq	Correction for a problem with sequences during indexing
2007/07/31: geneseq	icarus/db/geneseq.is
2007/07/30: pdb	Correction for the address of the USA download site
2007/07/30: pdb	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
2007/07/25: medline	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
2007/07/24: genbank embl 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
2007/07/24: pdb	icarus/db/pdb.it icarus/db/pdbmodel.it
2007/07/23: geneseq	Change to provide more information in fasta headers with geneseq sequences
2007/07/23: geneseq	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)
2007/07/18: uniprot ipi	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
2007/07/17: system	icarus/db/dbxref.i icarus/db/href.i
2007/06/29: chebi	schema update for release chebi 34 and fixes for several display problems
2007/06/29: chebi	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)
2007/06/28: system	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
2007/06/28: 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.
2007/06/25: system	icarus/db/standard.is
2007/06/22: ensembl_mysql	Correction for the links from ensembl to entrezgene
2007/06/22: ensembl_mysql	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
2007/06/21: embl	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
2007/06/20: srscheck	icarus/workflows/linkPhase.i
2007/06/20: embl	Fix for a problem where prisma would not remove obsolete files for the emblnew database
2007/06/20: embl	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
2007/06/18: system	icarus/db/dbxref.i icarus/db/href.i
2007/06/18: genecards	Fix for wrong hypertext link to ensembl
2007/06/18: genecards	icarus/db/genecards.is
2007/06/14: ensembl_mysql	Small changes for ensembl release 45
2007/06/14: ensembl_mysql	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
2007/06/13: kegg	icarus/db/lcommon.is
2007/06/08: uniprot ipi	Added hypertext links for the Web Resources in the comment field
2007/06/08: uniprot ipi	icarus/db/swissprot.is
2007/05/30: genecards	Change to allow for the new BIOMOL line in genecards
2007/05/30: genecards	icarus/db/genecards.is
2007/05/30: kegg	Latest version of kegg species mapping file
2007/05/30: kegg	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
2007/05/30: omim	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
2007/05/29: uniprot ipi	icarus/db/swisscommon.i icarus/db/swissprot.is
2007/05/29: genecards	Fix for a reformatcommand which might fail on linux systems
2007/05/29: genecards	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
2007/05/25: reactome	icarus/db/reactome.i icarus/db/reactome_schema.i
2007/05/25: genecards	Corrected a wrong defintions for the link to goterm
2007/05/25: genecards	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.
2007/05/25: kegg system	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
2007/05/10: entrezgene	icarus/db/entrezgene.is
2007/05/10: dbest	Modification to allow for the display of map submitter information
2007/05/10: dbest	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
2007/05/03: ensembl_mysql	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
2007/04/25: system	icarus/db/standard.is
2007/04/20: transfac	Fixed the binding site parsing so display fnuctions properly
2007/04/20: transfac	icarus/db/transfaccommon.is
2007/04/16: embl	removed a duplicate genomeProject production
2007/04/16: embl	icarus/db/embl.is
2007/04/12: geneticcode	Removed sorting from name index. Multiple values present due to database updates
2007/04/12: geneticcode	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
2007/04/12: kegg	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
2007/04/05: system	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
2007/04/03: system uniprot ipi	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
2007/04/03: entrezgene	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
2007/04/03: go_xml system	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")
2007/04/03: genecards	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
2007/03/28: system	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
2007/03/28: genbank embl refseq	icarus/db/gbemblcommon.is
2007/03/26: kegg	Fix for a problem with displaying html-ized GIDs in tables
2007/03/26: kegg	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
2007/03/21: system uniprot ipi	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.
2007/03/21: medline	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
2007/03/21: srscheck	icarus/workflows/getSystemLibs.i
2007/03/20: kegg	Updates species mapping file for the kegg databases
2007/03/20: kegg	icarus/db/kegg_species.i
2007/03/19: dbest	Change to allow for lower case sequence characters
2007/03/19: dbest	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.
2007/03/19: embl genbank refseq	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"
2007/03/09: reactome	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
2007/03/07: kegg	icarus/db/kegggenes.is
2007/03/07: system	Change to allow for the new CYGD reference in the latest release of uniprot
2007/03/07: system	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
2007/03/07: ensembl_mysql	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
2007/03/07: kegg	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
2007/03/06: dbest dbgss	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
2007/02/22: system	icarus/db/dbxref.i icarus/db/href.i
2007/02/21: userdna userprotein	Increased maxline to 500 to allow for longer header lines
2007/02/21: userdna userprotein	icarus/db/userdna.i icarus/db/userprotein.i
2007/02/20: kegg	Added Remark section for Reactions
2007/02/20: kegg	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
2007/02/20: ensembl_mysql emboss	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
2007/02/19: srscheck	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
2007/02/16: srscheck	icarus/workflows/coreCheckClasses.i
2007/02/13: pdb	Change so we no longer see the Broken Pipe error message when indexing pdb
2007/02/13: 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
2007/02/09: uniseq	icarus/db/uniseq.is
2007/02/07: uniest	Change to allow for refseq style Accession numbers
2007/02/07: uniest	icarus/db/uniest.is
2007/02/05: kegg	Changes to allow for the new Activity field in the kegg drug database
2007/02/05: kegg	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
2007/02/02: uniest unigene uniseq	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
2007/01/29: kegg	icarus/db/pathwaytar.it
2007/01/29: kegg	updated kegg species mapping file
2007/01/29: kegg	icarus/db/kegg_species.i
2007/01/25: system	Change so prisma will download the 2007 files for mesh
2007/01/25: system	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
2007/01/25: kegg	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
2007/01/25: reactome	icarus/db/reactome.i icarus/db/reactome_schema.i
2007/01/25: ensembl_mysql	Schema and database name changes for ensembl 42 (MySql)
2007/01/25: ensembl_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
2007/01/25: kegg	icarus/db/kegg_species.i
2007/01/17: genecards	Another fix to extend array to 50 elements
2007/01/17: genecards	icarus/db/genecards.is
2007/01/15: ensembl_mysql	Added change for OMIM identifier for linking
2007/01/15: ensembl_mysql	icarus/db/ensemblRDB.i
2007/01/15: system	Changed Interpro field used in Description View to use DF_Name
2007/01/15: system	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
2007/01/10: system uniprot ipi	icarus/db/dbxref.i icarus/db/swissprot.is
2007/01/04: srscheck	fix for srscheck/srsdo/srscheck reporting that virtual libs need rebuilding
2007/01/04: srscheck	icarus/workflows/moveIndicesPhase.i
2006/12/22: genecards	Minor fix for araay element out of bounds problem
2006/12/22: genecards	icarus/db/genecards.is
2006/12/21: system	Added href for DIP and changed HREF for Gene3D
2006/12/21: system	icarus/db/href.i
2006/12/21: uniprot ipi	Added link production for DIP, changed link production for Gene3D
2006/12/21: uniprot ipi	icarus/db/swissprot.is
2006/12/21: go_xml	Increased the limit on number of associations displayed,and fixed a layout problem with associations
2006/12/21: go_xml	icarus/db/go.is
2006/12/21: genecards	Some fixes to prevent parsing errors in the bioalma section
2006/12/21: genecards	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
2006/12/19: go_xml	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
2006/12/18: system	icarus/db/srsgen.i
2006/12/15: kegg	Added OMIM to list of db xrefs
2006/12/15: kegg	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
2006/12/15: ensembl_mysql	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
2006/12/13: genecards	icarus/db/genecardstar.it
2006/12/13: entrezgene	Fix for incorrect processing of some Interactions information
2006/12/13: entrezgene	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
2006/12/12: genecards system	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
2006/12/12: entrezgene	icarus/db/entrezgene.is
2006/12/05: uniprot ipi	Fix for GENE3d link in IPI which is different to the in UNIPROT
2006/12/05: uniprot ipi	icarus/db/swissprot.is
2006/12/04: uniprot ipi	Updated regularexpression for new version of Gene3D cross references
2006/12/04: uniprot ipi	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
2006/11/27: 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
2006/11/24: hmmer pfam	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
2006/11/20: system	icarus/db/dbxref.i icarus/db/href.i
2006/11/15: uniref	Added support for the uniparc ID in uniref
2006/11/15: 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.
2006/11/14: uniprot ipi	icarus/db/swissprot.is
2006/11/14: uniref	Change to allow for the new isSeed parameter in uniref members
2006/11/14: uniref	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
2006/11/10: kegg	icarus/db/lenzyme.is
2006/11/08: emboss	Corrections for some errors in the application definitions for dreg and fuzzpro
2006/11/08: emboss	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
2006/11/06: medline	icarus/db/medline.is
2006/11/06: geneseq	Improved display of patent assignee field
2006/11/06: geneseq	icarus/db/aageneseq.i icarus/db/geneseq.is
2006/11/03: kegg	Changes to allow for the new GLYCAN and COMPOUND lines in lreaction
2006/11/03: kegg	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
2006/11/03: kegg	icarus/db/kegg_species.i
2006/10/31: medline	Added comments about the different databases which make up medline in SRS
2006/10/31: medline	icarus/db/medline.i
2006/10/31: blast	Some changes for more reliable hypertext links to SRS entries for blast hits
2006/10/31: blast	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
2006/10/26: kegg	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
2006/10/26: kegg	icarus/db/pathway.is
2006/10/25: entrezgene	small change to fix a problem with pebmed hypertext links in the generif section
2006/10/25: entrezgene	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
2006/10/23: geneseq	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
2006/10/18: ensembl_mysql	icarus/db/ensemblRDB.i
2006/10/13: reactome	Some additional changes needed to handle some entries in reactome 18
2006/10/13: reactome	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
2006/10/12: system	icarus/db/mesh.it
2006/10/12: emboss	Updated our Emboss support to work with Emboss 4.0
2006/10/12: emboss	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
2006/10/12: system reactome	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
2006/10/12: kegg	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
2006/10/10: entrezgene	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
2006/10/09: kegg	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
2006/10/05: embl	icarus/db/emblwgsnewfiles.it
2006/10/04: chebi	Updates to work with the latest release of chebi (26)
2006/10/04: chebi	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
2006/10/03: geneseq	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
2006/10/02: 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
2006/09/28: system	icarus/db/dbxref.i
2006/09/15: kegg	Latest update of the kegg species mapping file
2006/09/15: kegg	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
2006/09/14: blast system	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
2006/09/13: system	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
2006/09/13: prosite system	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
2006/09/06: embl	icarus/db/emblnewfiles.it
2006/09/06: embl	Correction for wrong insertion of hypertext links to the enzyme database
2006/09/06: embl	icarus/db/embl.is
2006/09/06: genpept	updated/corrected hypertext link definitions used for dbxrefs in the comments section
2006/09/06: genpept	icarus/db/genpept.is
2006/08/25: iprmatches homologene	Added/updated images used for the display of iprmatches and homologene data
2006/08/25: iprmatches homologene	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
2006/08/24: ensembl_mysql	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
2006/08/24: system homologene	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
2006/08/23: kegg	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
2006/08/22: embl system	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
2006/08/22: entrezgene system	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.
2006/08/22: system	icarus/db/rdbaccess.i
2006/08/22: ensembl_mysql	Reformatted the file, and changed databases names to work with ensembl 40
2006/08/22: ensembl_mysql	icarus/db/ensemblRDB.i
2006/08/11: kegg	Added Reaction field for new format pathway files
2006/08/11: kegg	icarus/db/pathway.i
2006/08/11: blast	Changed the default setting of the Filter option of blast to have sequence filtering switched on
2006/08/11: blast	icarus/db/blastcommon.i
2006/08/11: embl	Fix for a problem which prevented the construction of contig sequences if tincaching is enabled
2006/08/11: embl	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
2006/08/10: entrezgene system	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
2006/08/01: rhdb	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
2006/07/28: uniprot ipi	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
2006/07/27: embl	icarus/db/embl.is
2006/07/24: geneseq	Minor change to use correct token for patent date in table display
2006/07/24: geneseq	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
2006/07/24: system kegg	icarus/db/href.i icarus/db/pathway.is
2006/07/20:	Added cvs header
2006/07/20:	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
2006/07/20: system	icarus/db/srsdb.i
2006/07/20: system	Contains links to pathosign, rzpd-protexp and ensembl_havana
2006/07/20: system	icarus/db/dbxref.i
2006/07/20: geneseq	Correction for hypertext link to the data provider
2006/07/20: geneseq	icarus/db/aageneseq.it icarus/db/nageneseq.it
2006/07/20: kegg	added support for the TARGET line in the kegg drug dataset
2006/07/20: kegg	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
2006/07/19: ensembl_mysql	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
2006/07/19: ensembl_mysql	srstags/srstags/web/views/ensemblproteinentry/proteinentry.jsp
2006/07/19: ensembl_mysql	Included ensembl virtual libraries in the package file used for installing ensembl
2006/07/19: ensembl_mysql	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
2006/07/19: srscheck	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"
2006/07/17: imgt	icarus/db/imgt.i
2006/07/17: kegg	Latest version of the kegg species mapping list used for kegggenes and lenzyme
2006/07/17: kegg	icarus/db/kegg_species.i
2006/07/17: chebi	Updated for new version of chebi (COMPOUND_CHILD_ID is changed to COMPOUND_ID).
2006/07/17: chebi	icarus/db/chebi_schema.i
2006/07/14: uniref	Change to allow for a change in the way the date is formatted in uniref
2006/07/14: 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
2006/07/14: kegg	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
2006/07/12: genecards	icarus/db/genecardstar.it
2006/07/12: hmmer	Corrected the way hmmsearch results are linked to uniprot data
2006/07/12: hmmer	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
2006/07/12: genecards	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
2006/07/11: system	icarus/db/href.i
2006/07/11: prosite	New file containing the date field to match the new prosite parser.
2006/07/11: prosite	srstags/srstags/web/views/prositeentry/prositeentry.jsp
2006/07/11: system	ProruleR has been added for use in prosite.
2006/07/11: system	icarus/db/href.i
2006/07/11: system	Updated with new uniprot link to rzpd-protexp
2006/07/11: system	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.
2006/07/11: prosite	icarus/db/prositedoc.i
2006/07/05: system	Added DF_DUPDate and DF_IUPDate srs fields for the new prosite.i file.
2006/07/05: system	icarus/db/srsgen.i
2006/07/05: prosite	Adjusted for new data format.
2006/07/05: prosite	icarus/db/prosite.i icarus/db/prosite.is
2006/06/29: ensembl_mysql	Added wildcard asterisk to searches for MIM owing to data change
2006/06/29: ensembl_mysql	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
2006/06/29: ensembl_mysql	icarus/db/ensemblRDB.i
2006/06/29: ensembl_mysql	Cosmetic changes
2006/06/29: ensembl_mysql	srstags/srstags/web/views/ensemblgeneentry/geneentry.jsp
2006/06/26: srscheck	Undo a mistake with CVS checkin of previous version
2006/06/26: srscheck	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
2006/06/23: genbank embl refseq geneseq	icarus/db/gbemblcommon.is icarus/db/geneseq.is
2006/06/22: srscheck	Fix for building readlinks when the chunkSize attribute is set.
2006/06/22: srscheck	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
2006/06/21: embl system	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
2006/06/19: uniprot ipi	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
2006/06/16: genbank refseq	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)
2006/06/15: kegg	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
2006/06/13: pdb	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
2006/06/12: system uniprot ipi	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
2006/06/12: system	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)
2006/06/09: embl	icarus/db/embl.is icarus/db/emblcommon.i
2006/06/06: ensembl_mysql	Updated for new ensembl schema changes
2006/06/06: ensembl_mysql	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
2006/06/06: kegg	icarus/db/lglycan.i
2006/06/05: ensembl_mysql	Updated for use with tfle due to the appearrance of the ensembl virtual database
2006/06/05: ensembl_mysql	icarus/db/UTRandCDS.il
2006/06/01: system	Correction for some inadvertently inserted end of line characters
2006/06/01: system	icarus/db/href.i
2006/05/31: uniprot ipi	Fix for matching . separators in h_des_enzyme
2006/05/31: uniprot ipi	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
2006/05/25: dbsts	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
2006/05/25: dbsts	icarus/db/dbsts.it
2006/05/25: blast fasta	Fix to make sure we do not build duplicate links
2006/05/25: blast fasta	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
2006/05/25: medline	srstags/srstags/web/views/medlineentry/medlineentry.jsp
2006/05/23: kegg	Latest species mapping list for Kegg databases
2006/05/23: kegg	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
2006/05/22: system	icarus/db/loader.i
2006/05/22: srscheck	Fix for some problems with the removeIndices option of srscheck
2006/05/22: 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
2006/05/18: embl genbank refseq	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
2006/05/18: system uniprot ipi	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
2006/05/18: genecards system	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
2006/05/16: geneseq	icarus/db/geneseqsupp.is
2006/05/15: srscheck	Fix for an unanticipated side effect of having virtual databases consisting of relational databases
2006/05/15: srscheck	icarus/workflows/coreCheckClasses.i
2006/05/11: ensembl_mysql	Updated after affy_* tables and columns were renamed to oligo_* by the Ensembl group
2006/05/11: ensembl_mysql	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
2006/05/11: ensembl_mysql	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
2006/05/08: kegg	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
2006/05/08: bind	icarus/db/bindinteraction.it
2006/05/08: kegg	Updated species mapping list for kegg
2006/05/08: kegg	icarus/db/kegg_species.i
2006/04/28: kegg	updated species mapping file for the kegg databases
2006/04/28: kegg	icarus/db/kegg_species.i
2006/04/27: ensembl_mysql	A clause was added in case alignment.colour was empty
2006/04/27: ensembl_mysql	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
2006/04/27: system prosite	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)
2006/04/27: ensembl_mysql	icarus/db/ensemblcore_schema.i
2006/04/27: ensembl_flat	Correction for the correct download location of the ensembl flatfiles
2006/04/27: ensembl_flat	icarus/db/ensembl.it
2006/04/27: transpath	Correction for the download location of the transpath files
2006/04/27: transpath	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
2006/04/27: ensembl_mysql	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
2006/04/25: kegg	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
2006/04/25: 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
2006/04/21: system	icarus/db/href.i
2006/04/20: genpept	Update to change to .gz file extension
2006/04/20: genpept	icarus/db/genpeptrelease.it icarus/db/gpnewfiles.it
2006/04/19: kegg	Allow for the new BRACKET lines in the lcoompound and lglycan data
2006/04/19: kegg	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
2006/04/19: kegg	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
2006/04/19: medline	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
2006/04/19: genpept	icarus/db/gpnewfiles.is
2006/04/13: system	Added drugR and drugMapR for useGG pathwya database
2006/04/13: system	icarus/db/href.i
2006/04/13: kegg	ldrug hyperlinks have been added to the pathway image maps
2006/04/13: kegg	icarus/db/pathway.is
2006/04/12: kegg	Updated for the latest data files so that the images show correctly.
2006/04/12: kegg	icarus/db/pathway.is
2006/04/11: kegg	Addition of new Pathway field
2006/04/11: kegg	srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2006/04/11: kegg	Changes made due to addition of new 'pathway' field
2006/04/11: kegg	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
2006/04/11: kegg	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.
2006/04/10: kegg	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.
2006/04/10: srscheck	icarus/workflows/moveIndicesPhase.i
2006/04/07: blocks	Changes to create links using Uniprot Accession rather than Id
2006/04/07: blocks	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
2006/04/07: unigene	icarus/db/unigene.is
2006/04/05: ensembl_mysql	The ID of pufferfish transcripts has been changed to ensembl ID
2006/04/05: ensembl_mysql	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.
2006/04/04: genbank embl refseq	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.
2006/04/04: ensembl_mysql	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
2006/04/04: ensembl_mysql	icarus/db/ensemblcore_schema.i
2006/04/04: ensembl_mysql	Changes made for ensembl virtual databases
2006/04/04: ensembl_mysql	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
2006/04/04: blocks	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
2006/04/03: transpath	icarus/db/transpath_datamodel.i icarus/db/transpath_gene.i
2006/04/03: geneticcode	Fix for URL to Genetic Codes homepage
2006/04/03: geneticcode	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.
2006/03/31: pfam	icarus/db/pfam.is
2006/03/30: kegg	Updated species list for the kegg databases
2006/03/30: kegg	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.
2006/03/29: transfac	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
2006/03/29: pfam	icarus/db/pfam.is srstags/srstags/web/views/pfamentry/refs.jsp
2006/03/28: taxonomy	Added indexing in parts for taxonomy
2006/03/28: taxonomy	icarus/db/taxonomy.i
2006/03/28: rhdb transfac unigene	Added sort tokens for various fiels to have better sort results
2006/03/28: rhdb transfac unigene	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
2006/03/28: system kegg	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
2006/03/28: uniprot	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)
2006/03/28: blast fasta system	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
2006/03/28: embl genbank	icarus/db/emblwgsrelease.i icarus/db/genbank.i
2006/03/28: transpath	Correction in database description
2006/03/28: transpath	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
2006/03/28: system	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
2006/03/28: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensemblcore_schema.i icarus/db/ensemblproteinmodel.i
2006/03/28: kegg	latest update for kegg species mapping file
2006/03/28: kegg	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
2006/03/27: srscheck	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.
2006/03/22: system	icarus/db/dbxref.i icarus/db/href.i
2006/03/22: unigene	New field added GENE_ID with links to the Entrez Gene database
2006/03/22: unigene	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.
2006/03/22: genecards	icarus/db/genecards.i icarus/db/genecards.is
2006/03/22: genecards	The BioAlma genes now have a new section to display them.
2006/03/22: genecards	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.
2006/03/22: system	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
2006/03/17: entrezgene	icarus/db/entrezgene.i icarus/db/entrezgene.is
2006/03/17: unilib	Correction to the way the link between unilib and taxonomy is build
2006/03/17: unilib	icarus/db/unilib.i
2006/03/15: geneticcode	updated url for NCBI genetic codes homepage
2006/03/15: geneticcode	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.
2006/03/15: embl genbank refseq	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
2006/03/15: geneseq	icarus/db/nageneseqtar.it
2006/03/14: uniprot	Added check so Last Annotation Update date field is not shown in IPI database
2006/03/14: uniprot	srstags/srstags/web/views/swissentry/swissentry.jsp
2006/03/13: system	A link to GenomeReviews has been added (for use in uniprot links)
2006/03/13: system	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
2006/03/13: uniprot	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
2006/03/13: uniprot	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
2006/03/13: pdb	icarus/db/pdbmodel.it
2006/03/13: uniprot ipi	The h_link production has been altered to contain the GenomeReviews link
2006/03/13: uniprot ipi	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
2006/03/10: entrezgene	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
2006/03/10: genbank embl refseq	icarus/db/gbemblcommon.is icarus/db/genbank.is
2006/03/10: geneseq	Correction for a wrong name for a tabletoken in 2 field defintions
2006/03/10: geneseq	icarus/db/geneseqsuppcommon.i
2006/03/10: geneseq	The 'description' and 'patent filing date' fields have been added to the aageneseq entry view
2006/03/10: geneseq	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
2006/03/10: geneseq	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
2006/03/07: system	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
2006/03/07: srscheck	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
2006/03/06: srscheck	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
2006/03/06: genbank refseq	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.
2006/03/06: genbank embl refseq	icarus/db/gbemblcommon.is
2006/03/03: system	Corrected ncbigiR link to include GENPEPT databank
2006/03/03: system	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
2006/03/02: blast fasta	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.
2006/03/02: embl	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
2006/03/01: ensembl_mysql iprmatches transfac	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.
2006/02/28: system	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
2006/02/28: kegg system	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.
2006/02/28: genbank embl refseq system	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
2006/02/28: dbest genpept	icarus/db/dbest.i icarus/db/genpeptrelease.i
2006/02/28: fasta	Small changes for slightly more robust performance
2006/02/28: fasta	icarus/db/fasta.is
2006/02/27: kegg	Update kegg species mapping file - this file is used for lenzyme, kegggenes_na and kegggenes_aa
2006/02/27: kegg	icarus/db/kegg_species.i
2006/02/17: srscheck	Corrected an error in a print command which caused srscheck to crash
2006/02/17: srscheck	icarus/workflows/srsCheckMain.i
2006/02/17: interpro	Correction for the hypertextlinks to the prints database which are displayed in interpro entries
2006/02/17: interpro	icarus/db/interpro.is
2006/02/17: system	add definition for links to BioCyc database for UNIPROT entries
2006/02/17: system	icarus/db/dbxref.i icarus/db/href.i
2006/02/16: interpro	Correction for the hypertext link to prodom data
2006/02/16: interpro	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
2006/02/16: prodom	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
2006/02/14: blast	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
2006/02/13: embl genbank refseq	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
2006/02/13: system	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
2006/02/10: blast	icarus/db/blast.is
2006/02/10: srscheck	added fix for args missing - and added diff from 81 branch
2006/02/10: srscheck	icarus/workflows/srsCheckMain.i
2006/02/10: kegg	fix for nested html tags in pathway field
2006/02/10: kegg	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)
2006/02/09: uniprot ipi	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
2006/02/09: rebase	icarus/db/rebase.i
2006/02/09: system	added GENPEPT to list of libs in hypertext links to GI numbers
2006/02/09: system	icarus/db/href.i
2006/02/08: kegg	Updated the kegg species mapping file for the latest species available in kegg
2006/02/08: 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
2006/02/07: genpept	icarus/db/genpeptrelease.it
2006/02/07: kegg	fix for ]+-e case # 9366
2006/02/07: kegg	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
2006/02/06: go_xml	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).
2006/02/02: uniprot ipi	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
2006/02/01: geneseq	icarus/db/geneseqsuppcommon.i
2006/02/01: system	Updated pubmedIdR
2006/02/01: system	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
2006/01/31: 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.
2006/01/31: genbank embl refseq	icarus/db/gbemblcommon.is
2006/01/30: prodom	Correction for the way the keyword field is indexd
2006/01/30: prodom	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.
2006/01/27: genecards	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.
2006/01/25: system	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
2006/01/25: genbank embl refseq	icarus/db/gbemblcommon.is
2006/01/23: ensembl_mysql	Urls have been updated after srs82 urls had inadvertently got checked in.
2006/01/23: ensembl_mysql	icarus/db/ensemblgenemodel.i
2006/01/20: bind	The parallelType has been updated from filesSize to files for use in indexing.
2006/01/20: bind	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
2006/01/19: srscheck	icarus/workflows/linkPhase.i
2006/01/17: transfac	Fix for references that don't have a last page
2006/01/17: transfac	icarus/db/transfaccommon.is
2006/01/17: reactome	The ecm and cme fields have been updated for the Reactome15 schema
2006/01/17: reactome	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
2006/01/13: genecards	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.
2006/01/10: transfac	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.
2006/01/09: system	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
2006/01/05: nrl3d	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
2006/01/05: kegg	icarus/db/kegg_species.i
2006/01/05: system	update mgdR link (Mouse Genome Database) to Jackson Laboratory
2006/01/05: system	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
2006/01/03: 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
2006/01/03: kegg	icarus/db/kegg_species.i
2005/12/29: pfam	Link annotations have been altered
2005/12/29: pfam	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
2005/12/23: 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
2005/12/22: uniref	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
2005/12/22: blocks	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
2005/12/22: system uniprot ipi	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
2005/12/22: domo	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)
2005/12/21: geneseq	icarus/db/geneseqsuppcommon.i
2005/12/14: ensembl_mysql	Adapted for Ensembl36
2005/12/14: ensembl_mysql	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
2005/12/09: embl	icarus/db/emblwgsrelease.i
2005/12/08: iprmatches	Improved layout, especially if using Firefox.
2005/12/08: iprmatches	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
2005/12/07: embl	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
2005/12/07: medline	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.
2005/12/07: genbank refseq	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.
2005/12/07: uniprot ipi	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
2005/12/06: genecards	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
2005/12/06: ensembl_flat system	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
2005/12/05: unilib	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
2005/12/05: uniref	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
2005/12/05: genecards	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
2005/12/02: pfam	icarus/db/pfamc.is
2005/12/02: system	update external link details to LinkHub at Yale Bioinformatics for UNIPROT entries
2005/12/02: system	icarus/db/dbxref.i icarus/db/href.i
2005/11/30: interpro	Added missing reference do resource object. This prevented prisma from downloading interpro
2005/11/30: interpro	icarus/db/interpro.i
2005/11/30: dbest	New JSP view
2005/11/30: dbest	srstags/srstags/web/views/dbestentry/dbest.jsp
2005/11/30: dbest	Updated for new entry view JSP
2005/11/30: dbest	icarus/db/dbest.i icarus/db/dbest.is
2005/11/25: ensembl_mysql	The link to locuslink (requiredlib attribute) has been changed to entrezgene.
2005/11/25: ensembl_mysql	icarus/lion/packages/ensemblRDB.ip
2005/11/25: kegg	Updated species list for the kegg databases
2005/11/25: kegg	icarus/db/kegg_species.i
2005/11/25: system	update EMBOSS url and version no.
2005/11/25: system	icarus/db/packages.i
2005/11/24:	Contain reactome15 updates
2005/11/24:	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
2005/11/24: entrezgene	icarus/db/entrezgene.i
2005/11/24: reactome	New JSPs for reactome15
2005/11/24: reactome	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
2005/11/24: reactome	srstags/srstags/web/views/reactomeentry/intercept.jsp
2005/11/24: reactome	New files for use with reactome15.
2005/11/24: reactome	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.
2005/11/24: ensembl	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
2005/11/22: ensembl_mysql	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
2005/11/22: system	icarus/db/quickSearchOptions.i
2005/11/18: uniprot	Correction for the unpackcomamnds for uniprot
2005/11/18: 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
2005/11/18: system	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.
2005/11/17: system	icarus/db/href.i
2005/11/17: entrezgene	Remove the gen fleid and geneName loadAttr, which cause the finder to malfunction
2005/11/17: entrezgene	icarus/db/entrezgene.i
2005/11/17: entrezgene	comment out printName attribute in Synonym Finder
2005/11/17: entrezgene	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
2005/11/16: system	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.
2005/11/16: hssp	icarus/db/hssp.i
2005/11/16: uniprot ipi	This patch corrects links from UniProt to the HSSP database
2005/11/16: uniprot ipi	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.
2005/11/15: kegg	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
2005/11/15: kegg	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.
2005/11/11: system transfac	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
2005/11/11: 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.
2005/11/11: system	srstags/srstags/web/WEB-INF/tags/section.tag
2005/11/11: entrezgene	add in Synonym Finder for Entrez Gene
2005/11/11: entrezgene	icarus/db/entrezgene.i
2005/11/11: iprmatches	javascript used by the iprmatches entry view
2005/11/11: iprmatches	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.
2005/11/09: system	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
2005/11/08: pdb	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
2005/11/08: geneseq	icarus/db/geneseqsupp.is
2005/11/07: iprmatches	Added a missing link definition for the link between teh signature subentry and the parent
2005/11/07: iprmatches	icarus/db/iprmatches.i
2005/11/04: transfac	A debug statement has been removed.
2005/11/04: transfac	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
2005/11/04: ensembl_mysql	icarus/lion/packages/ensemblRDB.ip
2005/11/04: ensembl_mysql	Change needed to work with the Mosquito data
2005/11/04: ensembl_mysql	icarus/db/exondatamodel.i
2005/11/04: kegg	Change to allow for the new Orthlogy field in the lreaction data
2005/11/04: kegg	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
2005/11/04: kegg	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
2005/11/04: uniprot ipi	icarus/db/swissprot.is
2005/11/04: emboss	Fix for a problem where the web interface erroneously reported that garnier had failed
2005/11/04: emboss	icarus/lion/emboss/garnier.i icarus/lion/emboss/garnier.is
2005/11/04: ensembl_mysql	Improved sequence display for ensembl exon sequences
2005/11/04: ensembl_mysql	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.
2005/11/04: srscheck	icarus/workflows/coreCheckClasses.i
2005/11/04: transfac	The seqlen production has been added for use in building tffactor feature images.
2005/11/04: transfac	icarus/db/transfaccommon.is
2005/11/04: transfac	The sequence length field (sl) has been added for use in building tffactor feature images.
2005/11/04: transfac	icarus/db/tffactor.i
2005/11/04: transfac	The sequence length field (sl) has been added.
2005/11/04: transfac	icarus/db/tffragment.i icarus/db/tfsite.i
2005/11/04: transfac	The sequence length field has been added.
2005/11/04: transfac	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.
2005/11/04: transfac	srstags/srstags/web/views/tffactorentry/tffactorentry.jsp
2005/11/04: transfac	This new file draws images of the factor features.
2005/11/04: transfac	srstags/srstags/web/views/tffactorentry/features.jsp
2005/11/04: ensembl_mysql	Updated link definitions for Ensembl 34
2005/11/04: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensemblcommon.i
2005/11/03: genecards	Added instructions for updating genecards using prisma
2005/11/03: genecards	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.
2005/11/03: geneseq system	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.
2005/11/03: system	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
2005/11/03: kegg	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
2005/11/03: kegg	icarus/db/kegg_species.i
2005/11/02: transfac	A new link to tfsite has been added.
2005/11/02: transfac	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
2005/11/02: transfac	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
2005/11/01: interpro iprmatches	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
2005/11/01: system	icarus/db/srsdb.i
2005/11/01: pfam	Added a default entry view to the pfamseed database
2005/11/01: pfam	icarus/db/pfamseed.i
2005/11/01: pfam	Added a jsp based entryview to pfamhmm
2005/11/01: pfam	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
2005/11/01: system	icarus/db/srsgen.i
2005/11/01: go_xml	Added commands so prisma will update the go (xml version) database
2005/11/01: go_xml	icarus/db/go.it
2005/11/01: medline	Added comments to the medline database definitions for use in the web interface
2005/11/01: medline	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
2005/11/01: pdb	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
2005/11/01: genecards	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
2005/11/01: transpath	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
2005/11/01: ensembl_mysql	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
2005/11/01: ensembl_mysql	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
2005/11/01: uniprot	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
2005/11/01: geneseq	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.
2005/11/01: entrezgene	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
2005/11/01: prints	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
2005/11/01: go_mysql	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
2005/11/01: system	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
2005/11/01: ensembl_mysql	icarus/db/ensemblproteinmodel.i
2005/11/01: genpept	Correction to the command by prisma to obtain the release number
2005/11/01: genpept	icarus/db/genpeptnew.it
2005/11/01: medline	Corrections for the download details for medline
2005/11/01: 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
2005/11/01: blast	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.
2005/11/01: embl	icarus/db/embl.is
2005/11/01: blast	Modification so patterns such as gnl\|gn_rem_geno\|AR689807 are recognised as genbank record
2005/11/01: blast	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
2005/11/01: system	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
2005/11/01: dbsts	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
2005/11/01: fasta	icarus/db/fasta.is
2005/11/01: prosite	increased stability for the commands used to update the prosite data for emboss
2005/11/01: prosite	icarus/db/prosite.it
2005/11/01: rebase	increased stability for the commands used to update the rebase data for embos and tacg
2005/11/01: rebase	icarus/db/rebase.it
2005/11/01: train	new view for the train database (a realtional database used for training)
2005/11/01: train	srstags/srstags/web/views/train/trainentry.jsp
2005/11/01: ensembl_mysql	update for Ensembl release 34
2005/11/01: ensembl_mysql	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.
2005/10/31: uniprot ipi	icarus/db/swissprot.is
2005/10/31: emboss	Fix for a problem where SRS would wrongly report that an emboss application had failed
2005/10/31: emboss	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
2005/10/31: system	icarus/db/href.i
2005/10/31:	adding EnsEMBL readme
2005/10/31:	README.ensemblRDB
2005/10/31: ensembl_mysql	changes for EnsEMBL version 34
2005/10/31: ensembl_mysql	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
2005/10/31: ensembl_mysql	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
2005/10/31: pdb	srstags/srstags/web/views/pdbentry/pdblinks.jsp
2005/10/28: chebi	adding chebi entry view
2005/10/28: chebi	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
2005/10/28: chebi	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
2005/10/28: transfac	icarus/db/tfgene.is
2005/10/27: transfac	Some missing concepts from the link to EPD have been added.
2005/10/27: transfac	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.
2005/10/27: transfac	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
2005/10/27: transfac	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
2005/10/27: transfac	icarus/db/tfsite.is
2005/10/27: transfac	tin_bs_fields production has been updated to work with transfac professional v9.3
2005/10/27: transfac	icarus/db/tfgene.is
2005/10/24: pdb	An new link to the enzyme database has been defined.
2005/10/24: pdb	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.
2005/10/24: pdb	icarus/db/pdb.is
2005/10/24: uniprot	DF_MoleculeType has been added in line with updates to data files.
2005/10/24: uniprot	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.
2005/10/24: uniprot ipi	icarus/db/swissprot.is
2005/10/21: unigene	Updating the ftp display information.
2005/10/21: unigene	icarus/db/unigene.it
2005/10/19: system	A Tffragment LibLoc has been added.
2005/10/19: system	icarus/db/srsdb.i
2005/10/19: system	Added hrefs for residR and comeR (Rea), tffragmentR (hoad) - updated from 81 branch.
2005/10/19: system	icarus/db/href.i
2005/10/19: transfac	Altered slightly to work with transfac professional v9.2
2005/10/19: transfac	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.
2005/10/19: system	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.
2005/10/19: transfac	icarus/db/tfcell.is
2005/10/19: transfac	This is a new file which contains productions common to the transfac group of libraries (tf*).
2005/10/19: transfac	icarus/db/transfaccommon.is
2005/10/19: transfac	Updated with 'more modern' JSP tags.
2005/10/19: transfac	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
2005/10/19: transfac	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.
2005/10/19: transfac	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
2005/10/19: transfac	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.
2005/10/12: unigene uniseq	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.
2005/10/12: uniprot	srstags/srstags/web/views/swissentry/swissentry.jsp
2005/10/12: blocks	hypertext links to uniprot changed form accession to id
2005/10/12: blocks	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.
2005/10/07: system	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.
2005/10/06: kegg	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.
2005/10/06: kegg	icarus/db/lenzyme.i icarus/db/lenzyme.is
2005/10/06: fasta	Correction for a token name specified for showing the fasta run details
2005/10/06: fasta	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
2005/10/06: fasta	icarus/db/fasta.is
2005/10/06: psiblast	minor correction for parsing psiblast results - preventing a non-fatal parsing error
2005/10/06: psiblast	icarus/db/psiblast.is
2005/10/06: psiblast	removed the -g option as it is no longer used by psiblast
2005/10/06: psiblast	icarus/db/psiblast.i
2005/10/05: system	Intact and Transpath library names changed.
2005/10/05: system	icarus/db/href.i
2005/10/04: emboss	Change to allow for more than 9 images to be generated by emboss programs
2005/10/04: emboss	icarus/lion/emboss/embossGraphFile.is
2005/10/04: go_xml	Updated for latest data release.
2005/10/04: go_xml	srstags/srstags/web/views/goentry/goentry.jsp
2005/10/04: go_xml go_mysql	Updated for new data release.
2005/10/04: go_xml go_mysql	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.
2005/10/03: kegg	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.
2005/10/03: kegg	icarus/db/kegggenome.i icarus/db/kegggenome.is
2005/10/03: system	New hrefs added for updated parsers: Intact, Genecards, GO (xml), Transpath.
2005/10/03: system	icarus/db/href.i
2005/10/03: kegg	Update of KEGG species file. Several new species acronyms have been added
2005/10/03: kegg	icarus/db/kegg_species.i
2005/09/23:	ribRowHighlightLightGreyBgColor and ribRowHighlightDarkGreyBgColor have been added for use in iprmatches list view.
2005/09/23:	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.
2005/09/22: geneseq	srstags/srstags/web/views/aageneseqentry/priority.jsp
2005/09/22: geneseq	Updated in line with priority.jsp being updated.
2005/09/22: geneseq	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.
2005/09/20: dbgss	icarus/db/dbgss.i
2005/09/20: dbgss	This file has been updated in line with the updates to the parser.
2005/09/20: dbgss	srstags/srstags/web/views/dbgssentry/dbgss.jsp
2005/09/20: dbgss	This parser has been updated making use of the standard parser more.
2005/09/20: dbgss	icarus/db/dbgss.is
2005/09/16: epd	A new dataclass field had been added. Values are standard or preliminary.
2005/09/16: epd	icarus/db/epd.i
2005/09/16: epd	A new token called dataclass has been added.
2005/09/16: epd	icarus/db/epd.is
2005/09/16: system	The DF_DataClass has been added for use in epd.
2005/09/16: system	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.
2005/09/16: epd	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.
2005/09/15: pfam	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.
2005/09/15: pfam	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.
2005/09/13: uniprot ipi	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.
2005/09/13: system	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.
2005/09/13: refseq	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).
2005/09/13: refseq	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.
2005/09/13: pfam	srstags/srstags/web/views/pfamentry/pfamentry.jsp
2005/09/13: pfam	New jsp entry view to display the pfamhmm data.
2005/09/13: pfam	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.
2005/09/13: pir	icarus/db/pir.i
2005/09/13: pfam	This file displays the citations, and is referenced from within pfamentry.jsp.
2005/09/13: pfam	srstags/srstags/web/views/pfamentry/refs.jsp
2005/09/12: pfam	New links have been added to prodom and prositedoc.
2005/09/12: pfam	icarus/db/pfamb.i
2005/09/12: blocks	The description has been updated with a new description of how BLOCKS is made currently.
2005/09/12: blocks	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.
2005/09/12: rebase	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.
2005/09/12: pfam	icarus/db/pfama.i
2005/09/09: epd	FTP and WWW urls have been added to this page for display purposes.
2005/09/09: epd	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.
2005/09/09: uniprot	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.
2005/09/09: blocks	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.
2005/09/09: pir	icarus/db/pir.is
2005/09/08: blocks	The ignore attribute has been removed from the syntax object.
2005/09/08: blocks	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.
2005/09/08: blocks	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.
2005/09/07: prosite	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.
2005/09/07: embl	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.
2005/09/07: uniprot	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.
2005/09/07: uniprot	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.
2005/09/07: rebase	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'.
2005/09/07: embl	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.
2005/08/26: system	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
2005/08/26: refseq	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.
2005/08/25: bind	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.
2005/08/24: dbest	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).
2005/08/24: genbank refseq	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.
2005/08/22: dbest	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
2005/08/18: system	icarus/db/srsgen.i
2005/08/15: system	Parses searches noew which contain multiple databases and also databases containing numbers (uniref family).
2005/08/15: system	logs/logcount.is
2005/08/12: embl genbank refseq	Changes neede to handle embl entries with multiple organism lines
2005/08/12: embl genbank refseq	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
2005/08/12: blast	icarus/db/blast.is
2005/08/11: ensembl_mysql	Updates for ensembl release 32
2005/08/11: ensembl_mysql	icarus/lion/packages/ensemblRDB.ip
2005/08/10: go_mysql	Added download instructions for the goterm (mysql) data for use with prisma
2005/08/10: go_mysql	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
2005/08/10: blocks	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
2005/08/10: prints	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
2005/08/10: prosite	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
2005/08/10: rebase	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
2005/08/10: system	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
2005/08/10: pfam system	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
2005/08/10: ipi	icarus/db/ipi.i
2005/08/10: uniprot	Corrected a misspelling in the names for the links subentries
2005/08/10: uniprot	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
2005/08/10: system	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
2005/08/10: iprmatches system	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
2005/08/10: ensembl_mysql	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
2005/08/10: kegg	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
2005/08/10: go_mysql	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
2005/08/09: uniprot ipi	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
2005/08/09: system	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
2005/08/09: genbank embl refseq genpept	icarus/db/gbemblcommon.is icarus/db/genpept.is
2005/08/09: go_mysql	DatabaseName short name was incorrect
2005/08/09: go_mysql	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
2005/08/05: interpro	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
2005/08/05: entrezgene	icarus/db/entrezgene.is
2005/08/05: ensembl_mysql	Changed query form to use correct field name and to search entrezgene instead of locuslink
2005/08/05: ensembl_mysql	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
2005/08/04: pfam	icarus/db/pfam.is icarus/db/pfamb.i
2005/08/02: pdbfinder	Change to allwo for the new "T-Alternates" line in the data
2005/08/02: pdbfinder	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
2005/08/02: ensembl_mysql	icarus/db/exondatamodel.i
2005/08/02: ensembl_mysql	The compara schema file is necessary to enable orthologue comparisons in ensembl
2005/08/02: ensembl_mysql	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
2005/07/29: genbank embl refseq	icarus/db/gbemblcommon.is
2005/07/27: fasta	Modified so ssearch now correctly displays the linked description and seqlength fields in the ssearch view.
2005/07/27: fasta	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
2005/07/27: system uniprot ipi	icarus/db/href.i icarus/db/swissprot.is
2005/07/26: genbank embl refseq	Updated feature length (ftl) productions to match all formats.
2005/07/26: genbank embl refseq	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
2005/07/21: bind	icarus/db/bindcommon.i
2005/07/21: go_mysql	fix for incorrect database short name in query form
2005/07/21: go_mysql	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
2005/07/20: system	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
2005/07/19: go_xml	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
2005/07/19: bind	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
2005/07/19: geneseq	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
2005/07/19: kegg	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
2005/07/19: uniest unigene uniseq	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
2005/07/19: uniprot ipi	icarus/db/swissprot.is
2005/07/19: taxonomy	Change to the trimming of trailing spaces
2005/07/19: taxonomy	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
2005/07/19: medline	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
2005/07/19: uniref	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)
2005/07/19: go_xml	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
2005/07/19: system	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
2005/07/19: unilib	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
2005/07/19: embl	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
2005/07/19: kegg	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
2005/07/19: entrezgene	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
2005/07/19: entrezgene	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.
2005/07/19: ensembl_mysql system	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
2005/07/19: kegg	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
2005/07/19: system	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.
2005/07/12: system	logs/loguse.is
2005/07/11: system	Updated to work properly in srs8.x
2005/07/11: system	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
2005/07/08: system	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.
2005/07/08: system	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.
2005/07/08: fasta	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.
2005/07/08: blast	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.
2005/07/08: blast	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
2005/07/08: fasta	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.
2005/07/06: uniref	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.
2005/07/06: uniref	icarus/db/uniref.is
2005/07/05: geneseq	IN:India has been added to the list of countries.
2005/07/05: geneseq	icarus/db/geneseq.is
2005/07/05: fasta	Updated with a new defaultView attribute (Library class) pointing to the FastaGraphical view.
2005/07/05: fasta	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.
2005/07/05: fasta	icarus/db/fastacommon.i
2005/07/05: fasta	Updated with new productions and a tin for use with the new FastaGraphical view.
2005/07/05: fasta	icarus/db/fasta.is
2005/07/05: blast	Updated with references to FASTA format databases so the view displays with all the relevant information.
2005/07/05: blast	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
2005/06/29: dbsts	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
2005/06/29: system	icarus/db/loader.i
2005/06/17: affymetrix	Added for NetAffx databases.
2005/06/17: affymetrix	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.
2005/06/17: system	icarus/db/dbxref.i
2005/06/09: entrezgene	go accession is now padded instead of being turned into a regular expression
2005/06/09: entrezgene	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.
2005/06/08: genbank embl refseq	icarus/db/gbemblcommon.is
2005/06/08: ensembl_mysql	fix for change in field name from DB_Name to TranslationDB_Name
2005/06/08: ensembl_mysql	srstags/srstags/web/views/chromosome/chromosome.jsp
2005/06/08: ensembl_mysql	fix for zebrafish sequences
2005/06/08: ensembl_mysql	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
2005/06/02: srscheck	icarus/workflows/coreCheckClasses.i
2005/06/02: srscheck	1. added further checking for whether searchName/fileType combination retrieves a correct list of files
2005/06/02: srscheck	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.
2005/06/02: srscheck	icarus/workflows/checkLocalFiles.i
2005/06/02: system	Added hypertext links to the feature keys.
2005/06/02: system	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
2005/06/02: srscheck	icarus/workflows/srsCheckMain.i
2005/06/02: srscheck	added further checking for whether searchName/fileType combination retrieves a correct list of files
2005/06/02: srscheck	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
2005/06/02: srscheck	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
2005/05/26: interpro	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
2005/05/26: system	icarus/db/quickSearchOptions.i
2005/05/26: domo hssp prodom	Added a loadercache for faster data retrieval for the description view
2005/05/26: domo hssp prodom	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
2005/05/26: 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
2005/05/26: ensembl_mysql system	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
2005/05/26: 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
2005/05/26: blast system	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
2005/05/26: kegg	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
2005/05/26: system	icarus/db/dbxref.i icarus/db/href.i
2005/05/26: taxonomy	Changes needed for the taxonomy entry view
2005/05/26: taxonomy	icarus/db/treemodel.i
2005/05/26: dbsts	Correction for a wrong tag closure
2005/05/26: dbsts	srstags/srstags/web/views/dbstsentry/primer.jsp
2005/05/26: kegg	Correction to the comment describing the database
2005/05/26: kegg	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
2005/05/26: entrezgene	srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2005/05/26: go_mysql	Improved performance for linking by using microparsing
2005/05/26: go_mysql	icarus/db/goparse.is icarus/db/goterms.i
2005/05/26: system	Removed a (harmless) duplicate presence of the LibLoc for entrezgene
2005/05/26: system	icarus/db/srsdb.i
2005/05/26: fasta	removed an erroneous double quote from the fasta command definition
2005/05/26: fasta	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
2005/05/23: genbank embl refseq	icarus/db/gbemblcommon.is
2005/05/20: uniest unigene uniseq	Added support for Macaca mulatta for the unigene/uniseq/uniest datasets
2005/05/20: uniest unigene uniseq	icarus/db/unigenespecies.i
2005/05/20: unigene	Added support for the new poly A field
2005/05/20: unigene	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
2005/05/20: kegg	icarus/db/kegg_species.i
2005/05/20: uniref	Allow for the fact that uniref now labels UniProt references as UniProtKB
2005/05/20: uniref	icarus/db/uniref.is
2005/05/20: geneseq	Change to make sure we display the entire content of the patent section line
2005/05/20: geneseq	icarus/db/aageneseq.i icarus/db/nageneseq.i
2005/05/19: system	Added a new package describing the Paracel BLAST suite of tools.
2005/05/19: system	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
2005/05/13: kegg	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.
2005/05/05: genbank refseq	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
2005/05/05: system	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
2005/05/05: embl	icarus/db/embl.is
2005/05/05: medline	Fix to address spaces in author names breaking hypertext links.
2005/05/05: medline	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
2005/05/05: uniprot	icarus/db/swisscommon.i
2005/05/03: genbank embl refseq	Modified the acc production to fix a parsing bug.
2005/05/03: genbank embl refseq	icarus/db/gbemblcommon.is
2005/05/03: bind	fix for bind pathway entry 13056 which contains an interaction id that doesn't exist
2005/05/03: bind	icarus/db/bindcommon_datamodel.i
2005/04/29: ensembl_mysql	Added a test to remove the dependency on having the GOGENPROD library enabled
2005/04/29: ensembl_mysql	icarus/db/ensemblgenemodel.i
2005/04/29: kegg	Corrected instructions in the pathway.i file for enabling pathway to work under Tomcat.
2005/04/29: kegg	icarus/db/pathway.i
2005/04/29: kegg	Link to DBlink corrected. Correct URL now used.
2005/04/29: kegg	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
2005/04/29: kegg	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
2005/04/29: kegg	icarus/db/kegggenes.i
2005/04/29: enzyme	removed unwanted text from cofactor display
2005/04/29: enzyme	srstags/srstags/web/views/enzymeentry/enzymeentry.jsp
2005/04/28: ensembl_mysql	added hypertextlinks for gene neighbours
2005/04/28: ensembl_mysql	srstags/srstags/web/views/ensemblgeneentry/neighbours.jsp
2005/04/28: kegg	Added several new Kegg species to the list of abbreviations
2005/04/28: kegg	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
2005/04/28: entrezgene	icarus/db/entrezgene.is
2005/04/28: genbank embl refseq	Removed debugging output from the acc production.
2005/04/28: genbank embl refseq	icarus/db/gbemblcommon.is
2005/04/28: kegg	added a spacer in Enzyme
2005/04/28: kegg	srstags/srstags/web/views/lglycanentry/lglycanlinks.jsp
2005/04/28: system	added geneID field
2005/04/28: system	icarus/db/srsgen.i
2005/04/28: ensembl	adding rat and mouse images for ensembl canned query pages
2005/04/28: ensembl	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
2005/04/28: kegg	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
2005/04/28: kegg	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
2005/04/28: ensembl_mysql	icarus/lion/packages/ensemblRDB.ip
2005/04/28: kegg	view fix for reaction/enzyme loader change
2005/04/28: kegg	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
2005/04/21: system	icarus/db/srsgen.i
2005/04/21: bind	Added additional fields (GenInfo Id, Molecule Type and Molecule Id) for the bind subunits
2005/04/21: bind	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
2005/04/21: pir	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
2005/04/21: prints	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
2005/04/21: uniseq	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
2005/04/21: entrezgene	srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2005/04/20: taxonomy	A completely new entryview for the taxonomy database
2005/04/20: taxonomy	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
2005/04/20: kegg	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
2005/04/20: medline	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
2005/04/20: clustalw	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
2005/04/20: entrezgene system	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
2005/04/20: fssp	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
2005/04/20: blast	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
2005/04/20: prosite	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
2005/04/20: go_mysql	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
2005/04/20: embl system	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
2005/04/20: system	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
2005/04/20: embl genbank refseq	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
2005/04/20: dssp	srstags/srstags/web/views/dsspentry/dsspentry.jsp
2005/04/20: emboss	Removed a "echo -n" commands as it is not supported on solaris 8
2005/04/20: emboss	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
2005/04/20: ensembl_mysql	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
2005/04/20: srscheck	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.
2005/04/14: kegg	icarus/db/pathway.i icarus/db/pathway.is
2005/04/11: pdb	Modified site production to handle SITE IDs with 4 characters.
2005/04/11: pdb	icarus/db/pdb.is
2005/04/08: psiblast	add in test entries for quality report tool test
2005/04/08: psiblast	icarus/db/psiblast.it
2005/04/07: uniest unigene uniseq	Added support for Schistoma japonicum and Phytophtora infestans for the unigene/uniseq/uniest databases
2005/04/07: uniest unigene uniseq	icarus/db/unigenespecies.i
2005/04/05: psiblast	Correction for wrong command definition
2005/04/05: psiblast	icarus/db/psiblast.i
2005/03/29: locuslink	Change to allow for "https" occuring in some urls in the locuslink data
2005/03/29: locuslink	icarus/db/locuslink.is
2005/03/29: prodom	Corrected the complete omission of hypertext links in the links section
2005/03/29: prodom	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.
2005/03/23: geneseq	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.
2005/03/17: clustalw	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 "]"
2005/03/16: kegg	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
2005/03/07: embl	icarus/db/emblnewfiles.is
2005/03/04: fssp	Hyperlinks from FSSP to FSSPmatches are generated if the FSSPmatches is enabled in SRS3D.
2005/03/04: fssp	icarus/db/fssp.is