markers display in e!
Ken Y. Clark
kclark at stein.cshl.org
Wed Mar 5 11:26:43 EST 2003
On Tue, 4 Mar 2003, Anne Lamblin (CCGB) wrote:
[snip]
> The problem that we are encountering right now is how to handle the
> markers (SSR and Markers)
> I looked at 2 examples:
> http://www.gramene.org/gramene/map/marker_view.cgi?marker_name=RM590
> http://www.gramene.org/gramene/map/marker_view.cgi?marker_name=C405
>
> I am wondering what are the steps you took to
> 1. get this info into e! schema (created new tables?)
[snip]
Anne-Francoise,
I'm JAPH[1], so I can only try to answer a subset of your questions.
As for the above question, we created some (presently very
denormalized) tables in Oracle to hold the marker details information.
This data was in AceDB before that. The "marker_view.cgi" script you
reference above (which I wrote) pulls data from these Oracle tables.
which I populated with information given to me by our curators. I
believe this data was extracted primarily from AceDB, but it could
have come from additional sources, too.
> I would welcome any help and pointers you can pass on.
> I would be most interested in the schema/tables that hold the input and
> output data and the modification of the pipeline to submit jobs related
> to markers mapping and display.
I'll attach the schema for the marker tables used by the
marker_view.cgi script. (The schema is for Oracle, but I can also
provide a MySQL version, if you like.) Again, they aren't very
normalized, and we intend to redesign these tables when time permits.
If the "display" of markers means anything to do with our genetic and
comparative maps, then I'll refer you to the CMap project (which I
also wrote), a part of GMOD:
http://www.gmod.org/cmap
HTH,
ky
[1]-Just Another Perl Hacker
-------------- next part --------------
--
-- Created by SQL::Translator::Producer::Oracle
-- Created on Mon Dec 9 16:59:58 2002
--
-- We assume that default NLS_DATE_FORMAT has been changed
-- but we set it here anyway to be self-consistent.
ALTER SESSION SET NLS_DATE_FORMAT = 'YYYY-MM-DD HH24:MI:SS';
--
-- Table: marker_accession
--
DROP TABLE marker_accession;
CREATE TABLE marker_accession (
accession_id number(11) DEFAULT '0' CONSTRAINT nn_accession_id01 NOT NULL,
genbank_accession varchar2(20) DEFAULT '' CONSTRAINT nn_genbank_accession NOT NULL,
CONSTRAINT pk_marker_accession PRIMARY KEY (accession_id)
);
--
-- Table: marker_accession_to_object
--
DROP TABLE marker_accession_to_object;
CREATE TABLE marker_accession_to_object (
accession_to_object_id number(11) DEFAULT '0' CONSTRAINT nn_accession_to_object_id NOT NULL,
accession_id number(11) DEFAULT '0' CONSTRAINT nn_accession_id02 NOT NULL,
table_name varchar2(50) DEFAULT '' CONSTRAINT nn_table_name NOT NULL,
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id NOT NULL,
CONSTRAINT pk_marker_accession_to_object PRIMARY KEY (accession_to_object_id)
);
CREATE INDEX accession_id_marker_accession_ on marker_accession_to_object (accession_id);
--
-- Table: marker_aflp
--
DROP TABLE marker_aflp;
CREATE TABLE marker_aflp (
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id02 NOT NULL,
name varchar2(50) DEFAULT NULL,
molecular_weight number(11) DEFAULT NULL,
germplasm varchar2(50) DEFAULT NULL,
adapter1_name varchar2(50) DEFAULT NULL,
adapter1_restriction varchar2(50) DEFAULT NULL,
adapter1_sequence varchar2(50) DEFAULT NULL,
adapter1_complement varchar2(50) DEFAULT NULL,
adapter2_name varchar2(50) DEFAULT NULL,
adapter2_restriction varchar2(50) DEFAULT NULL,
adapter2_sequence varchar2(50) DEFAULT NULL,
adapter2_complement varchar2(50) DEFAULT NULL,
primer1_name varchar2(50) DEFAULT NULL,
primer1_common_seq varchar2(50) DEFAULT NULL,
primer1_overhang varchar2(50) DEFAULT NULL,
primer2_name varchar2(50) DEFAULT NULL,
primer2_common_seq varchar2(50) DEFAULT NULL,
primer2_overhang varchar2(50) DEFAULT NULL,
species_id number(11) DEFAULT '0' CONSTRAINT nn_species_id01 NOT NULL,
CONSTRAINT pk_marker_aflp PRIMARY KEY (marker_id),
CONSTRAINT name_marker_aflp UNIQUE (name)
);
--
-- Table: marker_alias
--
DROP TABLE marker_alias;
CREATE TABLE marker_alias (
alias_id number(11) DEFAULT '0' CONSTRAINT nn_alias_id NOT NULL,
alias varchar2(50) DEFAULT NULL,
CONSTRAINT pk_marker_alias PRIMARY KEY (alias_id),
CONSTRAINT alias_marker_alias UNIQUE (alias)
);
--
-- Table: marker_alias_to_object
--
DROP TABLE marker_alias_to_object;
CREATE TABLE marker_alias_to_object (
alias_to_object_id number(11) DEFAULT '0' CONSTRAINT nn_alias_to_object_id NOT NULL,
alias_id number(11) DEFAULT '0' CONSTRAINT nn_alias_id02 NOT NULL,
table_name varchar2(50) DEFAULT '' CONSTRAINT nn_table_name02 NOT NULL,
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id03 NOT NULL,
CONSTRAINT pk_marker_alias_to_object PRIMARY KEY (alias_to_object_id)
);
CREATE INDEX alias_id_marker_alias_to_objec on marker_alias_to_object (alias_id);
--
-- Table: marker_bac_accession
--
DROP TABLE marker_bac_accession;
CREATE TABLE marker_bac_accession (
bac_accession_id number(11) DEFAULT '0' CONSTRAINT nn_bac_accession_id NOT NULL,
bac_accession varchar2(20) DEFAULT '' CONSTRAINT nn_bac_accession NOT NULL,
CONSTRAINT pk_marker_bac_accession PRIMARY KEY (bac_accession_id)
);
--
-- Table: marker_bac_accession_to_objec
--
DROP TABLE marker_bac_accession_to_object;
CREATE TABLE marker_bac_accession_to_object (
bac_accession_to_object_id number(11) DEFAULT '0' CONSTRAINT nn_bac_accession_to_object_id NOT NULL,
bac_accession_id number(11) DEFAULT '0' CONSTRAINT nn_bac_accession_id02 NOT NULL,
table_name varchar2(50) DEFAULT '' CONSTRAINT nn_table_name03 NOT NULL,
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id04 NOT NULL,
CONSTRAINT pk_marker_bac_accession_to_obj PRIMARY KEY (bac_accession_to_object_id)
);
CREATE INDEX accession_id_marker_bac_access on marker_bac_accession_to_object (bac_accession_id);
--
-- Table: marker_image
--
DROP TABLE marker_image;
CREATE TABLE marker_image (
image_id number(11) DEFAULT '0' CONSTRAINT nn_image_id NOT NULL,
file_name varchar2(50) DEFAULT NULL,
caption long,
width number(11) DEFAULT NULL,
height number(11) DEFAULT NULL,
CONSTRAINT pk_marker_image PRIMARY KEY (image_id)
);
--
-- Table: marker_image_to_object
--
DROP TABLE marker_image_to_object;
CREATE TABLE marker_image_to_object (
image_to_object_id number(11) DEFAULT '0' CONSTRAINT nn_image_to_object_id NOT NULL,
image_id number(11) DEFAULT '0' CONSTRAINT nn_image_id02 NOT NULL,
table_name varchar2(50) DEFAULT '' CONSTRAINT nn_table_name04 NOT NULL,
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id05 NOT NULL,
CONSTRAINT pk_marker_image_to_object PRIMARY KEY (image_to_object_id)
);
CREATE INDEX image_id_marker_image_to_objec on marker_image_to_object (image_id);
--
-- Table: marker_rapd
--
DROP TABLE marker_rapd;
CREATE TABLE marker_rapd (
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id06 NOT NULL,
name varchar2(50) DEFAULT NULL,
primer1 varchar2(50) DEFAULT NULL,
primer2 varchar2(50) DEFAULT NULL,
band_size number(8,2) DEFAULT NULL,
species_id number(11) DEFAULT '0' CONSTRAINT nn_species_id02 NOT NULL,
CONSTRAINT pk_marker_rapd PRIMARY KEY (marker_id),
CONSTRAINT name_marker_rapd UNIQUE (name)
);
--
-- Table: marker_reference
--
DROP TABLE marker_reference;
CREATE TABLE marker_reference (
reference_id number(11) DEFAULT '0' CONSTRAINT nn_reference_id NOT NULL,
reference varchar2(20) DEFAULT '' CONSTRAINT nn_reference NOT NULL,
CONSTRAINT pk_marker_reference PRIMARY KEY (reference_id)
);
--
-- Table: marker_reference_to_object
--
DROP TABLE marker_reference_to_object;
CREATE TABLE marker_reference_to_object (
reference_to_object_id number(11) DEFAULT '0' CONSTRAINT nn_reference_to_object_id NOT NULL,
reference_id number(11) DEFAULT '0' CONSTRAINT nn_reference_id02 NOT NULL,
table_name varchar2(50) DEFAULT '' CONSTRAINT nn_table_name05 NOT NULL,
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id07 NOT NULL,
CONSTRAINT pk_marker_reference_to_object PRIMARY KEY (reference_to_object_id)
);
CREATE INDEX reference_id_marker_reference_ on marker_reference_to_object (reference_id);
--
-- Table: marker_rflp
--
DROP TABLE marker_rflp;
CREATE TABLE marker_rflp (
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id08 NOT NULL,
name varchar2(50) DEFAULT NULL,
species_id number(11) DEFAULT '0' CONSTRAINT nn_species_id03 NOT NULL,
dna_treatment varchar2(50) DEFAULT NULL,
source_type varchar2(50) DEFAULT NULL,
source_germplasm varchar2(50) DEFAULT NULL,
source_tissue varchar2(50) DEFAULT NULL,
source_treatment varchar2(50) DEFAULT NULL,
vector varchar2(50) DEFAULT NULL,
vector_antibiotic_resistance varchar2(50) DEFAULT NULL,
fragment_size number DEFAULT NULL,
vector_excision_enzyme varchar2(50) DEFAULT NULL,
vector_primers varchar2(50) DEFAULT NULL,
CONSTRAINT pk_marker_rflp PRIMARY KEY (marker_id),
CONSTRAINT name_marker_rflp UNIQUE (name)
);
--
-- Table: marker_ssr
--
DROP TABLE marker_ssr;
CREATE TABLE marker_ssr (
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id09 NOT NULL,
name varchar2(50) DEFAULT NULL,
clone varchar2(50) DEFAULT NULL,
repeat_motif varchar2(50) DEFAULT NULL,
forward_primer varchar2(50) DEFAULT NULL,
reverse_primer varchar2(50) DEFAULT NULL,
anneal_temperature number(11) DEFAULT NULL,
product_size number(11) DEFAULT NULL,
source_germplasm varchar2(50) DEFAULT NULL,
remarks long,
species_id number(11) DEFAULT '0' CONSTRAINT nn_species_id04 NOT NULL,
CONSTRAINT pk_marker_ssr PRIMARY KEY (marker_id),
CONSTRAINT name_marker_ssr UNIQUE (name)
);
--
-- Table: marker_sts
--
DROP TABLE marker_sts;
CREATE TABLE marker_sts (
marker_id number(11) DEFAULT '0' CONSTRAINT nn_marker_id10 NOT NULL,
name varchar2(50) DEFAULT NULL,
primer1 varchar2(50) DEFAULT NULL,
primer2 varchar2(50) DEFAULT NULL,
reference varchar2(50) DEFAULT NULL,
species_id number(11) DEFAULT '0' CONSTRAINT nn_species_id05 NOT NULL,
CONSTRAINT pk_marker_sts PRIMARY KEY (marker_id),
CONSTRAINT name_marker_sts UNIQUE (name)
);
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