Index of /lite/2010-01-31

Icon  Name                               Last modified      Size  Description
[DIR] Parent Directory - [   ] go_20100131-termdb-summary.txt.gz 02-Feb-2010 12:05 393 [   ] go_20100131-obo-xml.dtd.gz 02-Feb-2010 12:05 1.1K [   ] go_20100131-assocdb-summary.txt.gz 02-Feb-2010 12:05 1.2K [   ] go_20100131-seqdb-summary.txt.gz 02-Feb-2010 12:05 1.2K [   ] go_20100131-rdf.dtd.gz 02-Feb-2010 12:05 1.6K [TXT] README 10-May-2011 14:57 5.8K [   ] go_20100131-schema-mysql.sql.gz 02-Feb-2010 12:05 16K [   ] go_20100131-termdb.obo-xml.gz 02-Feb-2010 12:05 2.5M [   ] go_20100131-termdb.rdf-xml.gz 02-Feb-2010 12:05 2.8M [   ] go_20100131-termdb.owl.gz 02-Feb-2010 12:05 3.2M [   ] go_20100131-termdb-tables.tar.gz 02-Feb-2010 12:05 6.3M [   ] go_20100131-termdb-data.gz 02-Feb-2010 12:05 6.4M [   ] go_20100131-assocdb.rdf-xml.gz 02-Feb-2010 12:05 29M [   ] go_20100131-utilities-src.tar.gz 02-Feb-2010 12:05 30M [   ] go_20100131-assocdb-tables.tar.gz 02-Feb-2010 12:05 62M [   ] go_20100131-assocdb-data.gz 02-Feb-2010 12:05 64M [   ] go_20100131-seqdb.fasta.gz 02-Feb-2010 12:05 75M [   ] go_20100131-seqdb-tables.tar.gz 02-Feb-2010 12:05 142M [   ] go_20100131-seqdb-data.gz 02-Feb-2010 12:05 145M

For full documentation see


releases are named


YYYYMM is the release date (the release export usually follows some

the DATASET is one of:

* termdb - a database containing just the information on the

term                        GO controlled vocab terms
term2term                   relationships between GO terms
term_definition             definitions of terms
dbxref                      external database identifier entities
term_dbxref                 links from terms to other databases
term_synonym                synonyms for terms
graph_path                  transitive closure (all paths) in graph

* assocdb - a database containing both the GO vocabulary and
associations between GO terms and gene products. This database
subsumes termdb. These are the extra tables that are populated:

gene_product                 gene or protein or entity annotated
association                  link between gene product and GO term
evidence                     evidence type and reference for an assoc
gene_product_count           recursive product counts per GO term

sequences associated with these gene products. This db subsumes the
two above. It populates these additional tables:

seq                          biological sequence
gene_product_seq             link between a product and a sequence
seq_dbxref                   external database links for a sequence

populate these at some point in the future.

have been removed. The IEA associations provide relatively little
value compared to the curated associations, and they slow querying
seqdb release.

the TYPE is either

at a later date.

.obo-xml - OBO XML Export. Currently ontology only

.owl - OWL Export. Currently ontology only


to load)


In this distribution, uncompreess the file:


Which contains the (MySQL ported) schema used in this release 

schema diagrams here:

Go to


you should use the files from the same release.


problem importing it:

tar -zxvf go-YYYYMM-TYPE-tables.gz
cd <releasedir>
echo "create database mygo" | mysql
cat *.sql | mysql mygo
mysqlimport -L mygo *.txt


mysql> load data infile

when using Winzip (thanks to Henrik Edgren for the tip

Windows users have any advice.



work on non mysql setups


TIP: for converting mysql dumps to postgres, try my2pg

Thanks to Joe Morris of Affymetrix for the tip





you can access the data using the perl API - see

OR look at the perl API release for the data release:

tar -zxvf go_YYYYMM-utilities_src.tar.gz
cd go_YYYYMM-utilities_src
cd perl-api
perldoc GO/

schema changes in a way to break old code


you can build a local AmiGO installation using the source code and
script and makefile in go-dev/sql


Email the go-database mail list; go to

And click on "Mail List" in the sidebar

Be sure to have read the rest of the database documentation before
asking a question