Cottongen

Data Template


Template	marker	download

Headers


Column	Description
* marker_name	Name of the marker.
* marker_type	Marker type such as SSR, RFLP, RAPD, STS, SCAR, overgo probe and Isozyme. Refer to the available marker_type page for each database.
* genus	The genus name of the organism from which the marker was developed.
* species	The species name of the organism from which the marker was developed. Enter 'sp.' to represent one unknown species, 'spp.' to represent multiple unknown species.
alias	Other names used for the marker. Multiple aliases, separated by a semicolon (;), can be added.
marker_locus	Name of the marker locus. Multiple loci, separated by a semicolon (;), can be added..
marker_sequence	Sequence of the marker when available. For SNP, it should be in the format of 5'flanking sequence[A/T] 3'flanking sequence.
GB_ID	Associated GenBank ID of the marker or the source of the marker (eg. EST).
dbSNP_ID	Associated dbSNP_ID. The submitted SNPs (SS) number should be used.
RS_ID	The refSNP (RS) number.
gene	Associated genes. Multiple genes, separated by a semicolon (;), can be added.
mRNA	Associated mRNAs. Multiple mRNAs, separated by a semicolon (;), can be added.
five_prime_flanking_seq	5' flanking sequence of SNP or Indel.
three_prime_flanking_seq	3' flanking sequence of SNP or Indel.
repeat_motif	Repeat motif for SSR markers.
snp_chip_name	SNP chip name when SNPs belong to a chip (the name should match 'name' in Library sheet. 'SNP_chip_ID' must be provided.
snp_chip_id	SNP ID for the specific SNP chip entered in 'SNP_chip_name'. It cannot be empty if 'SNP_chip_name' is provided.
restriction_enzyme	Restriction Enzyme used for CAPS marker or other markers that use restriction enzymes.
product_length	The PCR product length from the source species of the marker.
max_length	The maximum product size that have been observed.
min_length	The minimum product size that have been observed.
is_codominant	Yes if the marker is codominant, No otherwise.
PCR_condition	PCR condition for PCR-based markers.
screening_method	Gel type, % etc. (eg. 2% agarose) for PCR product visualization and any other screening methods for other types of markers.
monomorphic_population	The name of the mapping population of which the marker was monomorphic.
gel_picture_file_name	File name of the gel picture if available.
gel_picture_legend	Legend of the gel picture if available.
indel_seq	sequences of indel (eg. ATT).
alleles	Alleles for the SNP marker (eg. A/T).
comments	Any comments about the marker.
variety	The variety from which the marker was developed. It should match a 'stock_name' in the Stock sheet.
image	Image ID of any associated image (Detailed info in 'Image' sheet.) Multiple images, separated by comma, can be added.
contact	Contact person for the marker (Please provide the contact info of these researchers in 'Contact' sheet).
reference	Reference where the marker is originally described (pub_id), Multiple references, separated by comma, can be added.
~identifier	Special columns to store names and sequences of primers and probes. The column name should start with ~. An identifier must be either 'primer' or 'probe' , followed by a numerical number and 'name' or 'seq'. (e.g.) primer1_name, primer1_seq, primer2_name, primner2_seq ; probe1_name, probe1_seq, probe2_name, probe2_seq (More columns can be created when there are more than two primers and probes).
##property_name	Special columns (##) : followed by name of the custom property.

* Required field

cvterms


cv.name	cvterm.name
MAIN	SNP_chip
MAIN	alias
MAIN	comments
MAIN	filename
MAIN	indel_seq
MAIN	is_codominant
MAIN	legend
MAIN	marker_locus
MAIN	marker_type
MAIN	max_length
MAIN	min_length
MAIN	monomorphic_population
MAIN	pcr_condition
MAIN	product_length
MAIN	repeat_motif
MAIN	restriction_enzyme
MAIN	rs_id
MAIN	screening_method
MAIN	source
MAIN	ss_id
sequence	SNP
sequence	allele
sequence	associated_with
sequence	five_prime_flanking_region
sequence	gene
sequence	genetic_marker
sequence	mRNA
sequence	primer
sequence	probe
sequence	three_prime_flanking_region
relationship	adjacent_to
relationship	instance_of

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