================================================================================================ September 2004 ================================================================================================ Welcome to the Gene Ontology Consortium's Anonymous FTP server The Gene Ontology Consortium provides a collection of files via Anonymous FTP from ftp.geneontology.org and from an Anonymous CVS repository. Details about the GO Consortium can be obtained from the web at http://www.geneontology.org/ The FTP server is located at: ftp://ftp.geneontology.org/go/ To connect to the Anonymous CVS repository use a CVS client with the following directory options. In this example the user is first logged in and then checks out the complete repository (about 270 MB in size): cvs -d :pserver:anonymous@cvs.geneontology.org:/anoncvs login cvs -d :pserver:anonymous@cvs.geneontology.org:/anoncvs checkout go ================================================================================================ The following is a description of the directories, and the types of files within each, that are available from both the CVS and FTP servers. ------------------------------------------------------------------------------------------------ ./doc : documents, including abbreviations for database cross-references and their definitions, and other files with miscellaneous types of information - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./external2go : files that contain a mapping from an external system (e.g. EC classifications, Interpro, MetaCyc) to GO terms - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./gene-associations : files created though curation by a group or project (e.g. SGD, FlyBase, GO Annotations at EBI) that associate gene products with GO terms, including evidence codes, references, and other supporting information for the annotation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./gene-associations/readme : Readme files for the above mentioned gene-association files - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./GO_slims : files that contain a subset of GO terms, a selected set of high level terms from one, two, or three of the Gene Ontologies, particularly useful for reporting results of genome-level analyses; different GO_slims have been created for various purposes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./gp2protein : index files between database object ID and sequence IDs. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./meeting : Announcements, Agendas, and Meeting Programs for GO Users Meetings. Since 2007 all meeting information has been posted on the wiki.geneontology.org - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./meeting/minutes : Minutes from GO Consortium Meetings. Since 2007 all meeting information has been posted on the wiki.geneontology.org - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./numbers : Defines number ranges for particular projects and lists numbers which have been used. This is for internal curation projects only. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./ontology : Contains the three primary ontology files and the definitions file. Files are provided in OBO versions 1.0 and 1.2. All files are updated daily except those in the editors directory. The contents of that directory can change several times a day during active ontology development. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software : Contributed software from the GO Consortium. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/Python/mgibrowser : A GO term browser provided by the MGI group - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/SGD : Software from SGD group - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/SGD/geneAssociation : Perl scripts used by SGD to create their gene-association file. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/SGD/goAnnotation : Perl scripts for Oracle storage of GO associations - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/SGD/goPath : Perl scripts to parse ontology files and output child/parent flat file - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/utilities : Various utilities, including the script to create the GO Monthly Reports. The utilities subdirectory contains several of the scripts run nightly via cron in the GOC production environment. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./software/utilities/goview : Java used to create the go-diff daily messages that show changes in the ontologies - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./synonyms : Files to define synonym types and list synonyms for GO terms - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./teaching_resources : collection of posters, presentations and tutorials by contributed by members of the Consortium - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./www : document root for the GO web site (www.geneontology.org); contains all HTML files used for the GO web site - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ./xml : archive for XML files created by the Gene Ontology group at University of California, Berkeley. ================================================================================================ The following directories are only available from the Anonymous FTP site: ------------------------------------------------------------------------------------------------ MonthlyReports : Report detailing change to the ontologies - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - old-archive : Old files used by the GO Consortium before April 1999. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ontology-archive : Copy of the three ontology files from January 1, 2001 to the present.