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|
#######################################
# emboss.standard definition file
#######################################
#######################################
# This file is included in the EMBOSS distribution
# and installed automatically.
#
# The definitions are required by EMBOSS applications
# to use the EDAM annotations of ACD files and
# public data resources, and to make a set of
# public data servers available without the
# need for additional configuration.
############################################
#######################################
# Standard databases
#######################################
#######################################
# EBI Chemical Ontology (CHEBI)
#######################################
DBNAME chebi [
comment: "Chemical Entities of Biological Interest"
release: "93"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "none"
edamtpc: "0154 ! Small molecules"
edamdat: "0962 ! Small molecule report"
edamid: "1174 ! ChEBI ID"
edamfmt: "2196 ! OBO format"
]
#######################################
# Evidence codes ontology (ECO)
# used to define sequence database evidence
#######################################
DBNAME eco [
comment: "Evidence code ontology"
release: "2.02"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "none"
edamfmt: "2196 ! OBO format"
]
#######################################
# EDAM ontology (EMBRACE Data And Methods)
# used to annotate all ACD files
# and the Data Resource Catalogue
#######################################
DBNAME edam [
comment: "EMBRACE Data and Methods ontology"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME edam_data [
comment: "EMBRACE Data and Methods ontology (data)"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
dbalias: "edam"
namespace: "data|identifier"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME edam_format [
comment: "EMBRACE Data and Methods ontology (formats)"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
dbalias: "edam"
namespace: "format"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME edam_identifier [
comment: "EMBRACE Data and Methods ontology (identifiers)"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
dbalias: "edam"
namespace: "identifier"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME edam_operation [
comment: "EMBRACE Data and Methods ontology (operations)"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
dbalias: "edam"
namespace: "operation"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME edam_topic [
comment: "EMBRACE Data and Methods ontology (topics)"
release: "1.1"
type: "obo"
format: "obo"
method: "emboss"
dbalias: "edam"
namespace: "topic"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data"
# fields: "id acc nam isa des ns hasattr hasin hasout
# isid isfmt issrc"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
field: "hasattr ! identifier(s) from has_attribute relation(s)"
field: "hasin ! identifier(s) from has_input relation(s)"
field: "hasout ! identifier(s) from has_output relation(s)"
field: "isid ! identifier(s) from is_identifier_of relation(s)"
field: "isfmt ! identifier(s) from is_format_of relation(s)"
field: "issrc ! identifier(s) from is_source_of relation(s)"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
############################################
# Gene ontology (GO)
# used to annotate public sequence databases
############################################
DBNAME go [
comment: "Gene Ontology"
release: "1.1.3300"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des ns"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
taxon: "1 all"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME go_component [
comment: "Gene Ontology (cellular components)"
release: "1.1.3300"
type: "obo"
format: "obo"
method: "emboss"
namespace: "cellular_component"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des ns"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
taxon: "1 all"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME go_function [
comment: "Gene Ontology (molecular functions)"
release: "1.1.3300"
type: "obo"
format: "obo"
method: "emboss"
namespace: "molecular_function"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des ns"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
taxon: "1 all"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
DBNAME go_process [
comment: "Gene Ontology (biological processes)"
release: "1.1.3300"
type: "obo"
format: "obo"
method: "emboss"
namespace: "biological_process"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des ns"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
field: "ns ! namespace"
taxon: "1 all"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
#######################################
# Pathways ontology (PW)
#######################################
DBNAME pw [
comment: "Pathways ontology"
release: "12:06:2012 11:03"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "1 all"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
#######################################
# Relations ontology (RO)
# used to define OBO file relations
#######################################
DBNAME ro [
comment: "Relations ontology"
release: "20:03:2009 11:58"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
#######################################
# Sequence ontology (SO)
# used to define sequence features
#######################################
DBNAME so [
comment: "Sequence ontology"
release: "02:05:2012 11:08"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
#######################################
# Software ontology (SWO)
# used to define general software
# in collaboration with EDAM
#######################################
DBNAME swo [
comment: "Software ontology"
release: "12-jul-2012"
type: "obo"
format: "obo"
method: "emboss"
indexdirectory: "$emboss_standard/index"
directory: "$emboss_standard/data/OBO"
# fields: "id acc nam isa des"
field: "id ! identifier without the prefix"
field: "acc ! full name and any alternate identifier(s)"
field: "nam ! words in the name"
field: "isa ! parent identifier from is_a relation(s)"
field: "des ! words in the description"
taxon: "none"
edamtpc: "0089 ! Ontologies"
edamdat: "0966 ! Ontology term"
edamid: "1176 ! GO term ID"
edamfmt: "2196 ! OBO format"
]
#############################################
# Data Resource Catalogue DRCAT.dat
# lists all available public data resources
# with example queries and annotation
# using EDAM ontology terms to describe the
# resource, and also the data type, format
# and identifier for each query
#############################################
DBNAME drcat [
comment: "Data Resource Catalogue"
release: "alpha 1 21-jun-2011"
type: "resource"
format: "drcat"
method: "emboss"
indexdirectory: "$emboss_standard/index/"
directory: "$emboss_standard/data/"
# fields: "id acc nam des url cat edat efmt eid etpc xref
# qout qfmt qin qurl cc stat"
field: "id ! identifier without the prefix"
field: "acc ! any alternate identifier(s)"
field: "nam ! words in the name"
field: "des ! words in the description"
field: "url ! words in the main resource URL"
field: "cat ! category"
field: "edat ! EDAM data term(s) for query results"
field: "efmt ! EDAM format term(s) for query results"
field: "eid ! EDAM data term(s) for query identifier(s)"
field: "etpc ! EDAM topic term(s)"
field: "xref ! Data base cross-reference records"
field: "qout ! Query output data type"
field: "qfmt ! Query format name"
field: "qin ! Query identifier name(s)"
field: "qurl ! Query URLs"
field: "cc ! words in the comment(s)"
field: "rest ! REST service"
field: "soap ! SOAP service"
field: "stat ! status"
field: "xref ! Database cross-reference"
field: "taxid ! NCBI taxonomy identifier"
taxon: "none"
edamtpc: "0089 ! Ontologies"
]
#############################################
# NCBI taxonomy nodes.dmp and names.dmp
# lists all taxons in the public sequence databases
#############################################
DBNAME taxon [
comment: "NCBI taxonomy"
release: "July 2012"
type: "taxonomy"
format: "ncbi"
method: "embosstax"
indexdirectory: "$emboss_standard/index/"
directory: "$emboss_standard/data/TAXONOMY"
# fields: "id acc tax rnk up gc mgc"
field: "id ! identifier without the prefix"
field: "acc ! any alternate identifier(s)"
field: "tax ! taxon name"
field: "rnk ! taxon rank name"
field: "up ! parent taxon id"
field: "gc ! genetic code"
field: "mgc ! mitochondrial genetic code"
taxon: "1 ! all"
edamtpc: "0637 ! Taxonomy"
edamid: "1179 ! NCBI taxonomy ID"
edamdat: "3028 ! Taxonomic data"
]
################################################
# Servers providing standard sets of databases
################################################
######################
# SRS server at EBI
######################
SERVER srs [
method: "srswww"
type: "unknown"
url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
comment: "SRS from EBI"
serverversion: "7.1.3"
cachefile: "server.srs"
]
SERVER dkfz [
method: "srswww"
type: "sequence features text obo"
# url: "http://www.dkfz-heidelberg.de/srs/srs7131bin/cgi-bin/wgetz"
url: "http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz"
comment: "SRS from DKFZ Heidelberg"
serverversion: "7.1.3"
cachefile: "server.dkfz"
]
#######################
# ENSEMBL
#######################
SERVER ensembl [
method: "ensembl"
type: "sequence"
cachefile: "server.ensembl"
caseidmatch: "N"
comment: "Public Ensembl MySQL instance,
use for small-scale queries only."
field: "id ! identifier"
field: "eid ! Ensembl Exon stable identifier"
field: "pid ! Ensembl Translation stable identifier"
field: "tid ! Ensembl Transcript stable identifier"
field: "grp ! Ensembl Database Adaptor group"
format: "ensembl"
hasaccession: "N"
identifier: "id"
url: "mysql://anonymous@ensembldb.ensembl.org:5306/"
]
SERVER ensemblgenomes [
method: "ensembl"
type: "sequence"
cachefile: "server.ensemblgenomes"
caseidmatch: "N"
comment: "Public Ensembl Genomes MySQL instance,
use for small-scale queries only."
field: "id ! identifier"
field: "eid ! Ensembl Exon stable identifier"
field: "pid ! Ensembl Translation stable identifier"
field: "tid ! Ensembl Transcript stable identifier"
field: "grp ! Ensembl Database Adaptor group"
format: "ensembl"
hasaccession: "N"
identifier: "id"
url: "mysql://anonymous@mysql.ebi.ac.uk:4157/"
]
#######################
# DAS
#######################
SERVER das [
method: "das"
type: "sequence, features"
url: "http://www.dasregistry.org/das/"
comment: "DAS sequence/feature sources listed on the DAS registry"
cachefile: "server.dasregistry"
]
#######################
# BioMart
#######################
SERVER biomart [
method: "biomart"
type: "sequence"
url: "http://www.biomart.org:80/biomart/martservice"
cachefile: "server.biomart"
]
#######################
# MRS
#######################
SERVER mrs [
methodquery: "mrs"
type: "unknown"
url: "http://mrs.cmbi.ru.nl/mrs-5/search"
cachefile: "server.mrs"
serverversion: "MRS-5"
]
SERVER mrs4 [
methodquery: "mrs4"
type: "unknown"
url: "http://mrs.cmbi.ru.nl/mrs-web/plain.do"
cachefile: "server.mrs4"
serverversion: "MRS-4"
]
SERVER mrs3 [
methodquery: "mrs3"
type: "unknown"
url: "http://mrs.cmbi.ru.nl/mrs-3/plain.do"
cachefile: "server.mrs3"
serverversion: "MRS-3"
]
#######################
# Entrez at NCBI
#######################
SERVER entrez [
methodquery: "entrez"
type: "unknown"
cachefile: "server.entrez"
]
IFDEF EMBOSS_AXIS2C
#############################
# EBI's EB-eye search service
#############################
SERVER ebeye [
methodquery: "ebeye"
type: "text"
url: "http://www.ebi.ac.uk/ebisearch/service.ebi"
comment: "EB-eye text search service
that allows searching across EBI public databases"
cachefile: "server.ebeye"
]
###########################
# EBI's WsDbFetch service
###########################
SERVER wsdbfetch [
methodentry: "wsdbfetch"
type: "sequence, features, text, obo"
url: "http://www.ebi.ac.uk/ws/services/WSDbfetchDoclit"
comment: "EBI dbfetch webservices(SOAP)"
cachefile: "server.wsdbfetch"
]
ENDIF
###########################
# EBI's DbFetch service
###########################
SERVER dbfetch [
methodentry: "dbfetch"
type: "sequence, features, text, obo"
url: "http://www.ebi.ac.uk/Tools/dbfetch/"
comment: "EBI dbfetch webservices(REST)"
cachefile: "server.dbfetch"
]
##################################################################
# Resource definitions for the dbx indexing system.
##################################################################
RESOURCE dbxresource [
type: "Index"
idlen: "15"
acclen: "15"
svlen: "15"
deslen: "25"
orglen: "15"
keylen: "15"
]
RESOURCE taxresource [
type: "Index"
fields: "id acc tax rnk up gc mgc"
rnklen: "16"
idlen: "7"
uplen: "7"
taxlen: "120"
gclen: "2"
mgclen: "2"
]
RESOURCE emblresource [
type: "Index"
idlen: "15"
acclen: "15"
svlen: "15"
keylen: "80"
deslen: "75"
orglen: "75"
]
RESOURCE swissresource [
type: "Index"
idlen: "12"
acclen: "6"
svlen: "10"
deslen: "125"
keylen: "75"
orglen: "75"
despagesize: "4096"
keypagesize: "2048"
orgpagesize: "2048"
cachesize: "20000"
seccachesize: "100000"
]
RES pirresource [
type: "Index"
idlen: "6"
acclen: "6"
svlen: "10"
keylen: "25"
deslen: "15"
orglen: "35"
]
RESOURCE chebiresource [
type: "Index"
fields: "id acc nam isa des ns"
acclen: "400"
namlen: "125"
deslen: "50"
nslen: "20"
accpagesize: "16384"
nampagesize: "8192"
despagesize: "8192"
]
RES oboresource [
type: "Index"
fields: "id acc nam isa des ns"
acclen: "200"
namlen: "70"
deslen: "50"
nslen: "20"
accpagesize: "16384"
nampagesize: "16384"
despagesize: "4096"
]
RESOURCE sworesource [
type: "Index"
fields: "id acc nam isa des ns"
idlen: "60"
acclen: "100"
namlen: "150"
deslen: "50"
nslen: "20"
isalen: "50"
idpagesize: "16384"
accpagesize: "16384"
nampagesize: "16384"
despagesize: "4096"
isapagesize: "16384"
]
RESOURCE edamresource [
type: "Index"
fields: "id acc nam isa des ns hasattr hasin hasout
isid isfmt issrc"
acclen: "80"
namlen: "32"
deslen: "30"
isalen: "20"
accpagesize: "8192"
despagesize: "4096"
]
RESOURCE drcatresource [
type: "Index"
fields: "id acc nam des url cat taxid
edat efmt eid etpc xref
qout qfmt qin qurl rest soap cc stat"
idlen: "32"
acclen: "18"
qfmtlen: "30"
qinlen: "65"
qoutlen: "90"
qurllen: "30"
namlen: "20"
deslen: "20"
urllen: "25"
restlen: "20"
cclen: "40"
catlen: "60"
taxidlen: "6"
]
# Pagesize - this is the size of disc page blocks and is
# required by the 'dbx' indexing programs and 'method: emboss'
# We recommend a value of 2048
SET PAGESIZE 2048
SET SECPAGESIZE 512
# Cachesize - a cache of disc pages to be used by the 'dbx' indexing
# system and is required for 'method emboss'. It is the number of
# PAGESIZE or SECPAGESIZE blocks to cache and the initial size for the
# primary and secondary caches. We recommend a value of 20000. The
# secondary cache can be set separately as SECCACHESIZE. There is
# little to gain by reducing the values, but heavy I/O loads can be
# avoided by increasing them without exceeding the available physical
# memory for the indexing runs and other system load.
SET CACHESIZE 20000
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